DOI: 10.5061/dryad.9cnp5hqnx
title: Data from: Myristoyl's dual role in allosterically regulating and localizing Abl kinase

description: c-Abl kinase, a key signalling hub in many biological processes ranging
 from cell development to proliferation, is tightly regulated by two
 inhibitory Src homology domains. An N-terminal myristoyl-modification can
 bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the
 auto-inhibitory assembly. Activation is triggered by myristoyl release. We
 used molecular dynamics simulations to show how both myristoyl and the Src
 homology domains are required to impose the full inhibitory effect on the
 kinase domain, and reveal the allosteric transmission pathway at
 residue-level resolution. Importantly, we find myristoyl insertion into a
 membrane to thermodynamically compete with binding to c-Abl. Myristoyl
 thus not only localizes the protein to the cellular membrane, but membrane
 attachment at the same time enhances activation of c-Abl by stabilizing
 its pre-activated state. Our data put forward a model in which lipidation
 tightly couples kinase localization and regulation, a scheme that
 currently appears to be unique for this non-receptor tyrosine kinase.
description: Data was generated using Gromacs 2020 and 2018 and Plumed
 v2.5.2 Data was analyzed using Gromacs tools, Force
 Distribution Analysis (FDA) and ConAn We performed
 extensive Molecular Dynamics simulations under equilibrium conditions to
 compare the dynamics of different protein models and enhanced sampling
 methods such as Metadynamics to study helix conformational changes and
 Umbrella Sampling for Free Energy calculations of unbinding events. We
 analyzed contacts between protein domains and deciphered allosteric
 networks by looking at the forces between residue pairs.
description: # Data from: Myristoyl's dual role in allosterically regulating and
 localizing Abl kinase by de Buhr, Svenja and Gräter, Frauke This dataset
 on Abl kinase's allosteric regulation was created using Molecular
 Dynamics Simulations using Gromacs and Plumed, and analyzed using Gromacs
 tools, Plumed, FDA and ConAn. c-Abl kinase, a key signalling hub in many
 biological processes ranging from cell development to proliferation, is
 tightly regulated by two inhibitory Src homology domains. An N-terminal
 myristoyl-modification (Myr) can bind to a hydrophobic pocket in the
 kinase C-lobe, which stabilizes the auto-inhibitory assembly. Activation
 is triggered by Myr release. We used molecular dynamics simulations to
 show how both Myr and the Src homology (SH) domains are required to impose
 the full inhibitory effect on the kinase domain, and reveal the allosteric
 transmission pathway at residue-level resolution. In detail, we created
 Abl models with different conformations of the kinase C-terminal helix
 (alpha_I helix) critical for Myr binding and compared their equilibrium
 dynamics in the presence or absence of the SH domains or Myr. We
 deciphered allosteric pathways between the Myr binding site and the kinase
 active site by analyzing forces between protein residues. We futher
 investigated how the critical alpha_I helix changes its conformation using
 Metadynamics simulations and used output structures of these simulations
 for Free Energy calculation of Myr unbinding by means of Umbrella
 Sampling. Importantly, we find Myr insertion into a membrane to
 thermodynamically compete with binding to the Abl kinase domain. Myr thus
 not only localizes the protein to the cellular membrane, but membrane
 attachment at the same time enhances activation of c-Abl by stabilizing
 its pre-activated state. Our data put forward a model in which lipidation
 tightly couples kinase localization and regulation, a scheme that
 currently appears to be unique for this non-receptor tyrosine kinase. ##
 Description of the data and file structure The files include simulation
 input files (.mdp, .itp, .top, .gro, .tpr), as well as post-processing
 files (.xvg, .dat). Thorough documentation of the file formats can be
 accessed here:
 [https://manual.gromacs.org/documentation/2020/reference-manual/file-formats.html](https://manual.gromacs.org/documentation/2020/reference-manual/file-formats.html). The steps that were conducted to run the simulations are provided in text format or as executable bash scripts. There is a folder for each Abl model (kinase only and SH3-SH2-kinase models) that was simulated under equilibrium conditions, one folder containing the exact force field version used throughout the study and a folder for each larger analysis: force distribution analysis (FDA), Metadynamics, principal component analysis (PCA) and Umbrella sampling. The directory tree is provided at the bottom of this README. --- ### Folders named after protein models There is a folder containing the simulation and analysis files for each Abl model: * `SH3-SH2-KD_Myr, SH3-SH2-KD_noMyr, kinase_kinked_Myr, kinase_kinked_noMyr, kinase_straight_Myr, kinase_straight_noMyr, kinase_active`: * kinase-only models with a straight or kinked alpha_I helix * kinase-only model in an active conformation * SH3-SH2-kinase model * Each model was simulated with and without myristoyl (Myr). These folders contain the simulation files to be used with the Gromacs software for two sets of simulations that differ in the choice of thermostat. * simulation parameters (`.mdp`) * for the equilibration (nvt and npt ensemble) and production simulation * for details on the parameters refer to [https://manual.gromacs.org/2020/user-guide/mdp-options.html](https://manual.gromacs.org/2020/user-guide/mdp-options.html) * starting structures (`.gro`) detailing the atomic positions * the modelled protein with ATP, MG and Myr (system.gro), * inserted in the simulation box (system_box.gro), * after solvent addition (system_solv.gro), * after ionization/neutralization (system_solv_ions.gro) and * after energy minimization (system_em.gro) * topologies (`.top, .itp`) listing atom and corresponding connectivity parameters * master topology (topol.top) * include files (protein.itp, ATP.itp, MD.itp, MYR.itp) and position restraints (posre_* .itp) * index file (`index.ndx`) listing atom indices that belong to a certain group such as the protein, membrane, solvent, ions, etc. A subfolder for each replicate contains simulation start files an raw data files obtained through analysis with Gromacs tools and Plumed. The replicate numbers range from 11-20 and 21-30 for simulation set1 and set2, respectively. The simulation sets differ in the choice of temperature control method as detailed in the Methods section of the accompanying publication. * `.tpr` files contain all information needed for a single simulation and can be used to rerun each simulation. * `helicity.dat`: measure of helicity of Abl's alpha_I helix over time obtained using the Plumed alpharmsd collective variable * `rmsd_noIa_bb.xvg`: RMSD of Abl's kinase domain backbone atoms excluding the alpha_I helix over time * `rmsf.xvg`: RMSF for each residue of Abl's kinase domain The ConAn subfolder within the `SH3-SH2-KD_noMyr` folder contains files obtained through the ConAn software, which was used to analyze the contacts between Abl's kinase domain and SH2 domain. * subfolder for each replicate including * contact matrices for timepoints analyzed every 200 ps (`.dat` files) * `KD-SH2_dist.xvg`: distance between the kinase domain and SH2 domain over time * `SH2-KD_av_contacts_reps.csv`: average number of contacts for each replicate (rep) between the SH2 domain and the kinase domain excluding the alpha_I helix (core) and between the SH2 domain and the alpha_I helix (Ialpha) * `SH2-KD_contacts_native.csv`: number of contacts (count) between each residue pair (pair), indicated by residue indices * `SH2-KD_median_contacts_time.csv`: median number of contacts between kinase and SH2 domain over time ### FDA This folder contains the files needed for and obtained through the FDA analysis program. Refer to the FDA documentation for further details about the file types [https://github.com/HITS-MBM/gromacs-fda](https://github.com/HITS-MBM/gromacs-fda). * `diff* .pdb`: files obtained using the fda_graph tool, used to visualize force differences between indicated Abl models. Force differences are written as bonds exploiting the CONECT feature of pdb files. The files are named the following way: `diff_{comparison}_{property}_graph_{network}-{cutoff}.pdb` * comparison: force differences are calculated between two models, i.e. between kinase-only and SH3-SH2-kinase (`KD-whole`), between a kinase with a kinked and staight alpha_I helix (`kinked-straight`), or between a kinase with or without Myr (`Myr-noMyr`) * property: additional property of the compared models, i.e. do they contain Myr or not, is the alpha_I helix in the kinked or straight conformation * network: minimum size of a connected force difference cluster. If 'big' is written, only the biggest force difference cluster is written to the file * cutoff: force cutoff for the force differences between the models * `diff_{comparison}_{property}.pfr`: raw force differences between models. These files are obtained by subtracting forces written into the .pfr files of individual models using the the FDA.ipynb script (explained below). Files are named equivalently to the `diff* .pdb` files explained above. Contents are visualized with the help of the `diff* .pdb` files. * `FDA.ipynb`: jupyter notebook python script. Reads .pfr files and calculates the differences between two models * `input.pfi`: input parameters for FDA analysis * `.tga`: image of force differences (`diff* .pdb`) visualized and rendered using vmd * `.gro`, `.ndx`, `.tpr`, `.xtc` are files needed as input for FDA analysis * `.xtc` files are Gromacs trajectories containing only the protein atoms. They are written every 200 ps, excluding the first 1000 ns of the simulations. The files are named after each Abl model and replicate number. Files with 'concat' in their name contain the concatenated trajectories for each model. * `.gro`: Atomic structure file for each model including the protein atoms only, needed for force difference visualization * `.ndx`: Index files matching the protein only `.gro` file * `.tpr`: Run input file for the protein atoms only. * `.edr, .log, .trr`: Outputs of the FDA rerun containing the energies, logs and trajectories including atom forces and velocities, respectively * `.pfr`: Output obtained during FDA analysis. Contains forces between residue pairs * `start_fda.sh`: Bash script that submits an FDA run for each model * `steps`: commented list of commands performed during FDA analysis * `submit.sh`: Used by `start_fda.sh` script to submit the FDA run to a compute cluster. It includes the software version and exact command given to Gromacs FDA. * `vis_diff* _Fig1.tcl`: scripts to be used with the molecular visualization program vmd. Reads the `diff* .pfr` files and matching `.gro` files to display force differences ### ff This folder contains the force field used for all simulations: The Charmm36m force field, March 2019 version, for use with the Gromacs simulation software. Downloaded from the Mackarell Lab website: [http://mackerell.umaryland.edu/charmm_ff.shtml](http://mackerell.umaryland.edu/charmm_ff.shtml) ### Metadynamics This folder contains the input files and results of the Metadynamics simulations (`metad`) as well as simulation files of the equilibrium simulations performed using Metadynamics frames as start structures (`eq_after_metad`). The `metad` folder contains a protein reference structure and subfolders for each tested Metadynamics condition. Folders named `s* ` indicate the width/sigma of the added gaussians: s2 and s3 stand for a sigma of 0.02 and 0.03 nm, respectively. Subfolders therein mark the applied bias factor (`bf*`) and, if applicable, the number of replicate simulations. * `COLVAR`: Plumed output containing the value of the alpharmsd collective variable over time during the Metadynamics simulations * `HILLS`: Plumed output containing the height of the gaussians deposited during the Metadynamics simulations * `KD-SH2_dist.xvg`: Distance between the kinase domain and SH2 domain over time * `md.tpr`: Simulation input file * `plumed.dat`: File providing the input parameters for the Plumed software. The `eq_after_metad` folder includes results from simulations that were started from frames extracted form Metadynamics simulations. There is one folder for each replicate simulation named the following way: `s{sigma value}_bf{bias factor}_r{replicate}-fr{frame}ns` * sigma value`, `bias factor: gaussian width and bias factor that was used for the Metadynamics simulation from the the start frame for the simulation was taken * replicate: replicate number of the Metadynamics simulation * frame: time stamp at which the frame was extracted in ns The folders contain the topologies (`topol.top`), topology include files (`.itp`), extracted structure file (`frame_XXns.gro`) and run input files sufficient to restart the simulation (`md.tpr`). The ConAn subfolder contains contact matricies for each analyzed time step (1 ns intervals). ### PCA This folder contains the results of and all files necesarry to replicate the principal component analysis of kinase domain dynamics. * `autocorrelation.svg`: autocorrelations of the projections of the seperate simulation trajectories onto the first principal component * `average.pdb`: average structure obtained during covariance analysis using gmx covar * `bb-traj_combined.xtc`: combined simulation trajectories from all model and replicate simulations (seperate trajectories stored as `traj_{model}_{rep}.xtc` as described below) * `covar.txt`: log file written during gmx covar analysis * `eigenval.xvg`, `eigenvec.trr`: files containing the eigenvalues and eigenvectors, respectively, obtaining during the covariance analysis using gmx covar * `extreme_{model}_{rep}.pdb`: structure files showing the two extreme projections along a simulation trajectory. files are labeled by Abl model and replicate number * `KD_noIa_bb_ref.pdb`: reference structure for the kinase backbone atoms needed for analysis with gmx covar and anaeig * `modevectors_active-kinked_extreme.pse`: pymol session file, which generated the porcupine plots described below * `PCA_KDdyn_PC1_1av`: raw values (.csv files) and plots (.svg files) of the projection of the trajectories onto the first principal component when averaging across the whole trajectory * `PCA_KDdyn_PC1_ex100av400`: raw values (.csv files) and plots (.svg files) of the projection of the trajectories onto the first principal component when averaging across blocks of 400 ns length while leaving out 100 ns in between the averaging blocks * `PCA_KDdyn_PC1-3`: plot of the projection of the trajectories onto the first three principal components * `PCA_KDdyn_Pvals.csv`: list of all p-values calculated for the projections onto the first 3 principal components (PC) of the different model simulations. To evaluate the robustnest of the p-values and the impact of correlation between the data points, the p-values were obtained on different bases: * `all`: all data points * `discardXX`: discard the first XX ns of each simulation * `av`: averaging across all data points (1av) or across time blocks of XX ns length (avXX) * `exYYavXX`: averaging across blocks of XX ns length, while excluding XX ns in between the blocks * `everyXX`: using a datapoint every XX ns, discarding the rest * `porcupine_{model}.png`: porcupine plots for a kinase model with a kinked alpha_I helix and an active kinase model, both seperate and in comparison of the two models. the porcupine plots are obtained by reading the extreme projections of the model simulation trajectories with the modevectors.py script ([https://pymolwiki.org/index.php/Modevectors](https://pymolwiki.org/index.php/Modevectors)) * `proj.xvg`: projection of the combined trajectory onto the eigenvectors including the first 6 principal components * `proj_{model}_{rep}.xvg`: projection of single trajectories onto the eigenvectors of the combined trajectory. the files are labeled by Abl model and replicate number * `steps`: description of the steps performed during PCA including all Gromacs analysis commands and generation of porcupine plots * `traj_{model}_{rep}.xtc`: simulation trajectory files containing the backbone atoms of the kinase domains, one frame written every 2 ns ### setup\_analysis * `analysis_Fig1-B-E.sh`: Gromacs commands used to analyze kinase RMSD and RMSF and create the suitable index groups * `eq_sim_setup_steps.txt`: Gromacs commands used to setup the equilibrium simulations for each Abl model. Steps included topology generation, building the structure files, solvating and ionizing the simulation system, and energy minimization ### Umbrella This folder contains the files needed to replicate the Umbrella Sampling simulations and Free Energy calculations of Myr unbinding. * There a folders for SH3-SH2-kinase Abl models with different alpha_I helix conformations and for the membrane. Folders are named by the helix conformation or `membrane` in case of the membrane. `alphaI-kink` means the helix is in a kinked conformation as found in SH3-SH2-kinase crystal stuctures, `alphaI-straight` and `alphaI-unfold` means the helix assumes a straight or partially unfolded conformation as obtained by the Metadynamics simulations, and `delta-alphaIb` means that the helix was truncated starting at residue 518. These folders contain subfolders for equilibration, pulling and Umbrella Sampling simulations. * `eq`: equilibrium simulations started from Metadynamics frames to relax the structures in the absence of the Metadynamics bias. The included files are structure files (`.gro`), the topology (`topol_sys.top`) and topology include files (`.itp`), simulation parameters for energy minimization, NVT and NPT equilibration (`.mdp`), and the corresponding simulation start files (`.tpr`). The structure files include the extracted protein (`protein.gro`), myristoylated glycine (`GLYM.gro`), ATP (`ATP.gro`) and MG (`MG.gro`). The protein with the afore listed cofactors (`system.gro`) in its simulation box (`system_box.gro`) with the solvent (`system_solv.gro`) and neutralizing ions (`system_solv_ions.gro`) added and after energy minimization (`system_em.gro`). Subfolders for each simulation replicate (numbered) contain the simulation start file (`md.tpr`) for each run. * `pull`: simulations pulling Myr from its protein binding site or the membrane to accelerate the unbinding event. Simulation parameter and topology files are descibed above. Additionally the pulling parameters are included (`pull_md.mdp`). Numbered subfolders for each simulation replicate contain the last frame from the respective equilibrium simulation (`eq_md.gro`), and simulation start files for energy minimization (`pull_em.tpr`), equilibration (`nvt.tpr` and `npt.tpr`) and pulling simulation at the two different velocities 0.1 m/s and 0.05 m/s (`pull_md_0.1ms.tpr` and `pull_md_0.05ms.tpr`, respectively). * `umbrella`: simulations of the Umbrella Sampling windows and their analysis. * `{rep}_{velocity}_{frame}_pullx.xvg`: distances between the Myr binding site and Myr (collective variable) over time for each Umbrella Sampling window. Files are named by replicate number corresponding to the replicate numbers of equilibrium and pulling simulations, pulling velocity (`1` for 0.1 m/s and `05` for 0.05 m/s), and frame number of the extracted frame that was used for the respective Umbrella Sampling window. * `{rep}_{velocity}_{frame}.tpr`: simulation start file for each Umbrella Sampling window, named equivalently to the distance files described above * `analyze_umbrella_blocks.sh`: bash script to perform the block analysis to assess convergence of the Umbrella Sampling simulations * `analyze_umbrella_final.sh`: Gromacs command used for the final PMF calculation using PMF wham * `bsProfs_{start}-{end}ns.xvg`: PMF profiles for each bootstrap along the distance collective variable, provided for each block and for the final analysis including simulation time 80-200 ns. Blocks are labeled by their start and end time in ns. * `bsResult_{start}-{end}ns.xvg`: average PMF profile and standard deviation obtained through bootstrapping. * `frames.dat`: list of frames all extracted frames used to start Umbrella Sampling simulations * `histo_{start}-{end}.xvg`: histograms showing coverage across the distance collective variable * `profile_{start}-{end}.xvg`: average PMF profiles over the diatnce between Myr and its binding site * `pullx_files.xvg`, `tpr_files`: list of the distance and simulation start files of all Umbrella Sampling windows, needed for gmx wham analysis * `Abl_Myr_pull_setup`: text file including all Gromacs commands used to setup the simulations pulling Myr out of its protein binding site * `analyze_umbrella.sh`: bash script used to run the weighted histogram analysis method (gmx wham) analysis * `start_umbrella.sh`: bash script to automatically start the simulations of Umbrella Sampling windows * `umbrella_md.mdp`: simulation parameters applied during the Umbrella Sampling windows * `umbrella_npt.mdp`: simulation parameters applied while equilibrating the extracted Umbrella Sampling frames * `umbrella_sampling steps`: text file listing the steps performed to extract frames from the Myr pulling simulations along the distance collective variable and setup the Umbrella Sampling simulations * `umbrella_submit.sh`: submission script to run the Umbrella Sampling windows including equilibration --- ## Description of files used for each result figure in the accompanying publication (DOI: 10.7554/eLife.85216) ### Fig 2: In the folders for each Abl model: * Simulation parameters * .tpr files: start file for each simulation, can be used to replicate each simulation within machine precision * .xvg files: raw numerical data for figure panels B, E * panel B: rmsf.xvg * panel E: rmsd_noIa_bb.xvg 'PCA' folder: * raw data for panel C and D ### Fig 3: Data deposited in 'FDA' folder * backbone trajectories (.xtc), FDA input parameters (input.pfi) and output (.pfr), force differences for visualization (diff* .pdb) ### Fig 4: Contact matrices for each time point in 'ConAn' subfolder * native contacts stored in 'SH3-SH2-KD_noMyr' folder * contacts after Metadnymics stored in 'Metadynamics/eq_after_metad' folder, subfolders are named by sigma (s), bias factor (bf), replicate (r) and timepoint of the extracted frame during Metadnymics (fr) ### Fig 5: Within 'Umbrella' folder for each Abl model: * Simulation files for equilibration ('eq' folder) and pulling ('pull' folder) simulations: parameters .mdp, structure .gro, topologies .top/.itp, start file .tpr * Simulation start files (.tpr) and force trace (* \_pullf.xvg) for each sampling window, PMF trace and bootstraps as well as the histograms ('umbrella' folder) ### Figure Supplements: * Fig 1: file helicity.dat in folder for each Abl model * Fig 3+4: additional FDA analysis, see main Fig 2 * Fig 5: KD-SH2_dist.xvg files in 'SH3-SH2-KD_noMyr' folder (panel A/equilibrium distance) and 'Metadnymics/metad' folder (panel B/Metadynamics distance, subfolders named by sigma, bias factor and replicate number) * Fig 6: block analysis for main Fig 2 * Fig 7: same data as main Fig 2, seperated by Set * Fig 8: block analysis for main Fig 5 --- ## Directory tree ``` |- README.md +---FDA | \---FDA | diff_KD-whole_Myr.pfr | diff_KD-whole_Myr_graph_3-100.pdb | diff_KD-whole_Myr_graph_3-20.pdb | diff_KD-whole_Myr_graph_3-30.pdb | diff_KD-whole_Myr_graph_3-40.pdb | diff_KD-whole_Myr_graph_3-50.pdb | diff_KD-whole_Myr_graph_3-60.pdb | diff_KD-whole_Myr_graph_3-70.pdb | diff_KD-whole_Myr_graph_3-80.pdb | diff_KD-whole_Myr_graph_3-90.pdb | diff_KD-whole_Myr_graph_big-100.pdb | diff_KD-whole_Myr_graph_big-20.pdb | diff_KD-whole_Myr_graph_big-30.pdb | diff_KD-whole_Myr_graph_big-40.pdb | diff_KD-whole_Myr_graph_big-50.pdb | diff_KD-whole_Myr_graph_big-60.pdb | diff_KD-whole_Myr_graph_big-70.pdb | diff_KD-whole_Myr_graph_big-80.pdb | diff_KD-whole_Myr_graph_big-90.pdb | diff_KD-whole_noMyr.pfr | diff_KD-whole_noMyr_graph_3-100.pdb | diff_KD-whole_noMyr_graph_3-20.pdb | diff_KD-whole_noMyr_graph_3-30.pdb | diff_KD-whole_noMyr_graph_3-40.pdb | diff_KD-whole_noMyr_graph_3-50.pdb | diff_KD-whole_noMyr_graph_3-60.pdb | diff_KD-whole_noMyr_graph_3-70.pdb | diff_KD-whole_noMyr_graph_3-80.pdb | diff_KD-whole_noMyr_graph_3-90.pdb | diff_KD-whole_noMyr_graph_big-100.pdb | diff_KD-whole_noMyr_graph_big-20.pdb | diff_KD-whole_noMyr_graph_big-30.pdb | diff_KD-whole_noMyr_graph_big-40.pdb | diff_KD-whole_noMyr_graph_big-50.pdb | diff_KD-whole_noMyr_graph_big-60.pdb | diff_KD-whole_noMyr_graph_big-70.pdb | diff_KD-whole_noMyr_graph_big-80.pdb | diff_KD-whole_noMyr_graph_big-90.pdb | diff_kinked-straight_Myr.pfr | diff_kinked-straight_Myr_graph_3-100.pdb | diff_kinked-straight_Myr_graph_3-20.pdb | diff_kinked-straight_Myr_graph_3-30.pdb | diff_kinked-straight_Myr_graph_3-40.pdb | diff_kinked-straight_Myr_graph_3-50.pdb | diff_kinked-straight_Myr_graph_3-60.pdb | diff_kinked-straight_Myr_graph_3-70.pdb | diff_kinked-straight_Myr_graph_3-80.pdb | diff_kinked-straight_Myr_graph_3-90.pdb | diff_kinked-straight_Myr_graph_big-100.pdb | diff_kinked-straight_Myr_graph_big-20.pdb | diff_kinked-straight_Myr_graph_big-30.pdb | diff_kinked-straight_Myr_graph_big-40.pdb | diff_kinked-straight_Myr_graph_big-50.pdb | diff_kinked-straight_Myr_graph_big-60.pdb | diff_kinked-straight_Myr_graph_big-70.pdb | diff_kinked-straight_Myr_graph_big-80.pdb | diff_kinked-straight_Myr_graph_big-90.pdb | diff_kinked-straight_noMyr.pfr | diff_kinked-straight_noMyr_graph_3-100.pdb | diff_kinked-straight_noMyr_graph_3-20.pdb | diff_kinked-straight_noMyr_graph_3-30.pdb | diff_kinked-straight_noMyr_graph_3-40.pdb | diff_kinked-straight_noMyr_graph_3-50.pdb | diff_kinked-straight_noMyr_graph_3-60.pdb | diff_kinked-straight_noMyr_graph_3-70.pdb | diff_kinked-straight_noMyr_graph_3-80.pdb | diff_kinked-straight_noMyr_graph_3-90.pdb | diff_kinked-straight_noMyr_graph_big-100.pdb | diff_kinked-straight_noMyr_graph_big-20.pdb | diff_kinked-straight_noMyr_graph_big-30.pdb | diff_kinked-straight_noMyr_graph_big-40.pdb | diff_kinked-straight_noMyr_graph_big-50.pdb | diff_kinked-straight_noMyr_graph_big-60.pdb | diff_kinked-straight_noMyr_graph_big-70.pdb | diff_kinked-straight_noMyr_graph_big-80.pdb | diff_kinked-straight_noMyr_graph_big-90.pdb | diff_kinkedMyr-straightnoMyr.pfr | diff_kinkedMyr-straightnoMyr_graph_3-100.pdb | diff_kinkedMyr-straightnoMyr_graph_3-20.pdb | diff_kinkedMyr-straightnoMyr_graph_3-30.pdb | diff_kinkedMyr-straightnoMyr_graph_3-40.pdb | diff_kinkedMyr-straightnoMyr_graph_3-50.pdb | diff_kinkedMyr-straightnoMyr_graph_3-60.pdb | diff_kinkedMyr-straightnoMyr_graph_3-70.pdb | diff_kinkedMyr-straightnoMyr_graph_3-80.pdb | diff_kinkedMyr-straightnoMyr_graph_3-90.pdb | diff_Myr-noMyr_kinked.pfr | diff_Myr-noMyr_kinked_graph_3-100.pdb | diff_Myr-noMyr_kinked_graph_3-20.pdb | diff_Myr-noMyr_kinked_graph_3-30.pdb | diff_Myr-noMyr_kinked_graph_3-40.pdb | diff_Myr-noMyr_kinked_graph_3-50.pdb | diff_Myr-noMyr_kinked_graph_3-60.pdb | diff_Myr-noMyr_kinked_graph_3-70.pdb | diff_Myr-noMyr_kinked_graph_3-80.pdb | diff_Myr-noMyr_kinked_graph_3-90.pdb | diff_Myr-noMyr_kinked_graph_big-100.pdb | diff_Myr-noMyr_kinked_graph_big-20.pdb | diff_Myr-noMyr_kinked_graph_big-30.pdb | diff_Myr-noMyr_kinked_graph_big-40.pdb | diff_Myr-noMyr_kinked_graph_big-50.pdb | diff_Myr-noMyr_kinked_graph_big-60.pdb | diff_Myr-noMyr_kinked_graph_big-70.pdb | diff_Myr-noMyr_kinked_graph_big-80.pdb | diff_Myr-noMyr_kinked_graph_big-90.pdb | diff_Myr-noMyr_straight.pfr | diff_Myr-noMyr_straight_graph_3-100.pdb | diff_Myr-noMyr_straight_graph_3-20.pdb | diff_Myr-noMyr_straight_graph_3-30.pdb | diff_Myr-noMyr_straight_graph_3-40.pdb | diff_Myr-noMyr_straight_graph_3-50.pdb | diff_Myr-noMyr_straight_graph_3-60.pdb | diff_Myr-noMyr_straight_graph_3-70.pdb | diff_Myr-noMyr_straight_graph_3-80.pdb | diff_Myr-noMyr_straight_graph_3-90.pdb | diff_Myr-noMyr_straight_graph_big-100.pdb | diff_Myr-noMyr_straight_graph_big-20.pdb | diff_Myr-noMyr_straight_graph_big-30.pdb | diff_Myr-noMyr_straight_graph_big-40.pdb | diff_Myr-noMyr_straight_graph_big-50.pdb | diff_Myr-noMyr_straight_graph_big-60.pdb | diff_Myr-noMyr_straight_graph_big-70.pdb | diff_Myr-noMyr_straight_graph_big-80.pdb | diff_Myr-noMyr_straight_graph_big-90.pdb | diff_Myr-noMyr_whole-full.pfr | diff_Myr-noMyr_whole_graph_3-100.pdb | diff_Myr-noMyr_whole_graph_3-20.pdb | diff_Myr-noMyr_whole_graph_3-30.pdb | diff_Myr-noMyr_whole_graph_3-40.pdb | diff_Myr-noMyr_whole_graph_3-50.pdb | diff_Myr-noMyr_whole_graph_3-60.pdb | diff_Myr-noMyr_whole_graph_3-70.pdb | diff_Myr-noMyr_whole_graph_3-80.pdb | diff_Myr-noMyr_whole_graph_3-90.pdb | diff_Myr-noMyr_whole_graph_big-100.pdb | diff_Myr-noMyr_whole_graph_big-20.pdb | diff_Myr-noMyr_whole_graph_big-30.pdb | diff_Myr-noMyr_whole_graph_big-40.pdb | diff_Myr-noMyr_whole_graph_big-50.pdb | diff_Myr-noMyr_whole_graph_big-60.pdb | diff_Myr-noMyr_whole_graph_big-70.pdb | diff_Myr-noMyr_whole_graph_big-80.pdb | diff_Myr-noMyr_whole_graph_big-90.pdb | FDA.ipynb | input.pfi | KD-whole_Myr_3_50-70-90pN_aochalky-t15.tga | KD-whole_Myr_big_30-40pN_aochalky-t15.tga | KD-whole_noMyr_3_50-70-90pN_aochalky-t15.tga | KD-whole_noMyr_big_30-40pN_aochalky-t15.tga | kinase_kinked_Myr.edr | kinase_kinked_Myr.gro | kinase_kinked_Myr.log | kinase_kinked_Myr.ndx | kinase_kinked_Myr.pfr | kinase_kinked_Myr.tpr | kinase_kinked_Myr.trr | kinase_kinked_Myr_11.xtc | kinase_kinked_Myr_12.xtc | kinase_kinked_Myr_13.xtc | kinase_kinked_Myr_14.xtc | kinase_kinked_Myr_15.xtc | kinase_kinked_Myr_16.xtc | kinase_kinked_Myr_17.xtc | kinase_kinked_Myr_18.xtc | kinase_kinked_Myr_19.xtc | kinase_kinked_Myr_20.xtc | kinase_kinked_Myr_21.xtc | kinase_kinked_Myr_22.xtc | kinase_kinked_Myr_23.xtc | kinase_kinked_Myr_24.xtc | kinase_kinked_Myr_25.xtc | kinase_kinked_Myr_26.xtc | kinase_kinked_Myr_27.xtc | kinase_kinked_Myr_28.xtc | kinase_kinked_Myr_29.xtc | kinase_kinked_Myr_30.xtc | kinase_kinked_Myr_concat.xtc | kinase_kinked_noMyr.edr | kinase_kinked_noMyr.gro | kinase_kinked_noMyr.log | kinase_kinked_noMyr.ndx | kinase_kinked_noMyr.pfr | kinase_kinked_noMyr.tpr | kinase_kinked_noMyr.trr | kinase_kinked_noMyr_11.xtc | kinase_kinked_noMyr_12.xtc | kinase_kinked_noMyr_13.xtc | kinase_kinked_noMyr_14.xtc | kinase_kinked_noMyr_15.xtc | kinase_kinked_noMyr_16.xtc | kinase_kinked_noMyr_17.xtc | kinase_kinked_noMyr_18.xtc | kinase_kinked_noMyr_19.xtc | kinase_kinked_noMyr_20.xtc | kinase_kinked_noMyr_21.xtc | kinase_kinked_noMyr_22.xtc | kinase_kinked_noMyr_23.xtc | kinase_kinked_noMyr_24.xtc | kinase_kinked_noMyr_25.xtc | kinase_kinked_noMyr_26.xtc | kinase_kinked_noMyr_27.xtc | kinase_kinked_noMyr_28.xtc | kinase_kinked_noMyr_29.xtc | kinase_kinked_noMyr_30.xtc | kinase_kinked_noMyr_concat.xtc | kinase_straight_Myr.edr | kinase_straight_Myr.gro | kinase_straight_Myr.log | kinase_straight_Myr.ndx | kinase_straight_Myr.pfr | kinase_straight_Myr.tpr | kinase_straight_Myr.trr | kinase_straight_Myr_11.xtc | kinase_straight_Myr_12.xtc | kinase_straight_Myr_13.xtc | kinase_straight_Myr_14.xtc | kinase_straight_Myr_15.xtc | kinase_straight_Myr_16.xtc | kinase_straight_Myr_17.xtc | kinase_straight_Myr_18.xtc | kinase_straight_Myr_19.xtc | kinase_straight_Myr_20.xtc | kinase_straight_Myr_21.xtc | kinase_straight_Myr_22.xtc | kinase_straight_Myr_23.xtc | kinase_straight_Myr_24.xtc | kinase_straight_Myr_25.xtc | kinase_straight_Myr_26.xtc | kinase_straight_Myr_27.xtc | kinase_straight_Myr_28.xtc | kinase_straight_Myr_29.xtc | kinase_straight_Myr_30.xtc | kinase_straight_Myr_concat.xtc | kinase_straight_noMyr.edr | kinase_straight_noMyr.gro | kinase_straight_noMyr.log | kinase_straight_noMyr.ndx | kinase_straight_noMyr.pfr | kinase_straight_noMyr.tpr | kinase_straight_noMyr.trr | kinase_straight_noMyr_11.xtc | kinase_straight_noMyr_12.xtc | kinase_straight_noMyr_13.xtc | kinase_straight_noMyr_14.xtc | kinase_straight_noMyr_15.xtc | kinase_straight_noMyr_16.xtc | kinase_straight_noMyr_17.xtc | kinase_straight_noMyr_18.xtc | kinase_straight_noMyr_19.xtc | kinase_straight_noMyr_20.xtc | kinase_straight_noMyr_21.xtc | kinase_straight_noMyr_22.xtc | kinase_straight_noMyr_23.xtc | kinase_straight_noMyr_24.xtc | kinase_straight_noMyr_25.xtc | kinase_straight_noMyr_26.xtc | kinase_straight_noMyr_27.xtc | kinase_straight_noMyr_28.xtc | kinase_straight_noMyr_29.xtc | kinase_straight_noMyr_30.xtc | kinase_straight_noMyr_concat.xtc | kinked-straight_Myr_3_50-70-90pN_aochalky-t15.tga | kinked-straight_noMyr_3_50-70-90pN_aochalky-t15.tga | Myr-noMyr_kinked_3_50-70-90pN_aochalky-t15.tga | Myr-noMyr_straight_3_50-70-90pN_aochalky-t15.tga | Myr-noMyr_whole-full_3_50-70-90pN_aochalky-t15.tga | SH3-SH2-KD_Myr.edr | SH3-SH2-KD_Myr.gro | SH3-SH2-KD_Myr.log | SH3-SH2-KD_Myr.ndx | SH3-SH2-KD_Myr.pfr | SH3-SH2-KD_Myr.tpr | SH3-SH2-KD_Myr.trr | SH3-SH2-KD_Myr_11.xtc | SH3-SH2-KD_Myr_12.xtc | SH3-SH2-KD_Myr_13.xtc | SH3-SH2-KD_Myr_14.xtc | SH3-SH2-KD_Myr_15.xtc | SH3-SH2-KD_Myr_16.xtc | SH3-SH2-KD_Myr_17.xtc | SH3-SH2-KD_Myr_18.xtc | SH3-SH2-KD_Myr_19.xtc | SH3-SH2-KD_Myr_20.xtc | SH3-SH2-KD_Myr_21.xtc | SH3-SH2-KD_Myr_22.xtc | SH3-SH2-KD_Myr_23.xtc | SH3-SH2-KD_Myr_24.xtc | SH3-SH2-KD_Myr_25.xtc | SH3-SH2-KD_Myr_26.xtc | SH3-SH2-KD_Myr_27.xtc | SH3-SH2-KD_Myr_28.xtc | SH3-SH2-KD_Myr_29.xtc | SH3-SH2-KD_Myr_30.xtc | SH3-SH2-KD_Myr_concat.xtc | SH3-SH2-KD_noMyr.edr | SH3-SH2-KD_noMyr.gro | SH3-SH2-KD_noMyr.log | SH3-SH2-KD_noMyr.ndx | SH3-SH2-KD_noMyr.pfr | SH3-SH2-KD_noMyr.tpr | SH3-SH2-KD_noMyr.trr | SH3-SH2-KD_noMyr_11.xtc | SH3-SH2-KD_noMyr_12.xtc | SH3-SH2-KD_noMyr_13.xtc | SH3-SH2-KD_noMyr_14.xtc | SH3-SH2-KD_noMyr_15.xtc | SH3-SH2-KD_noMyr_16.xtc | SH3-SH2-KD_noMyr_17.xtc | SH3-SH2-KD_noMyr_18.xtc | SH3-SH2-KD_noMyr_19.xtc | SH3-SH2-KD_noMyr_20.xtc | SH3-SH2-KD_noMyr_21.xtc | SH3-SH2-KD_noMyr_22.xtc | SH3-SH2-KD_noMyr_23.xtc | SH3-SH2-KD_noMyr_24.xtc | SH3-SH2-KD_noMyr_25.xtc | SH3-SH2-KD_noMyr_26.xtc | SH3-SH2-KD_noMyr_27.xtc | SH3-SH2-KD_noMyr_28.xtc | SH3-SH2-KD_noMyr_29.xtc | SH3-SH2-KD_noMyr_30.xtc | SH3-SH2-KD_noMyr_concat.xtc | start_fda.sh | steps | submit.sh | vis_diff_KD-whole_Myr_Fig1.tcl | vis_diff_KD-whole_noMyr_Fig1.tcl | vis_diff_kinked-straight_Myr_Fig1.tcl | vis_diff_kinked-straight_noMyr_Fig1.tcl | vis_diff_Myr-noMyr_kinked_Fig1.tcl | vis_diff_Myr-noMyr_straight_Fig1.tcl | vis_diff_Myr-noMyr_whole-full_Fig1.tcl | +---ff | \---charmm36-mar2019.ff | atomtypes.atp | cmap.itp | ffbonded.itp | ffnonbonded.itp | forcefield.doc | forcefield.itp | gb.itp | ions.itp | merged.arn | merged.c.tdb | merged.hdb | merged.n.tdb | merged.r2b | merged.rtp | merged.vsd | nbfix.itp | old_c36_cmap.itp | spc.itp | spce.itp | tip3p.itp | tip4p.itp | watermodels.dat | +---kinase_active | \---kinase_active | +---Set1 | | | ATP.itp | | | MG.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | step6.0_minimization.mdp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---12 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---13 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---14 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---15 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---16 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---17 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---18 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | +---19 | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | | | \---20 | | md.tpr | | npt.tpr | | nvt.tpr | | | \---Set2 | | ATP.itp | | MG.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | step6.0_minimization.mdp | | system_em.gro | | topol.top | | | +---21 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---22 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---23 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---24 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---25 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---26 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---27 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---28 | | md.tpr | | npt.tpr | | nvt.tpr | | | +---29 | | md.tpr | | npt.tpr | | nvt.tpr | | | \---30 | md.tpr | npt.tpr | nvt.tpr | +---kinase_kinked_Myr | \---kinase_kinked_Myr | +---Set1 | | | ATP.itp | | | index.ndx | | | MG_ion.itp | | | MYR.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_MYR.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---12 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---13 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---14 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---15 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---16 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---17 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---18 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---19 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | \---20 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---Set2 | | ATP.itp | | index.ndx | | MG_ion.itp | | MYR.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_MYR.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | system_em.gro | | topol.top | | | +---21 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---22 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---23 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---24 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---25 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---26 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---27 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---28 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---29 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---30 | helicity.dat | md.tpr | npt.tpr | nvt.tpr | rmsd_noIa_bb.xvg | rmsf.xvg | +---kinase_kinked_noMyr | \---kinase_kinked_noMyr | +---Set1 | | | ATP.itp | | | index.ndx | | | MG_ion.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---12 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---13 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---14 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---15 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---16 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---17 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---18 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---19 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | \---20 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---Set2 | | ATP.itp | | index.ndx | | MG_ion.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | system_em.gro | | topol.top | | | +---21 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---22 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---23 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---24 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---25 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---26 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---27 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---28 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---29 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---30 | helicity.dat | md.tpr | npt.tpr | nvt.tpr | rmsd_noIa_bb.xvg | rmsf.xvg | +---kinase_straight_Myr | \---kinase_straight_Myr | +---Set1 | | | ATP.itp | | | index.ndx | | | MG.itp | | | MYR.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_MYR.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---12 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---13 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---14 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---15 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---16 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---17 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---18 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---19 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | \---20 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---Set2 | | ATP.itp | | index.ndx | | MG.itp | | MYR.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_MYR.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | system_em.gro | | topol.top | | | +---21 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---22 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---23 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---24 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---25 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---26 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---27 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---28 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---29 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---30 | helicity.dat | md.tpr | npt.tpr | nvt.tpr | rmsd_noIa_bb.xvg | rmsf.xvg | +---kinase_straight_noMyr | \---kinase_straight_noMyr | +---Set1 | | | ATP.itp | | | index.ndx | | | MG.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---12 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---13 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---14 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---15 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---16 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---17 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---18 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---19 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | \---20 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---Set2 | | ATP.itp | | index.ndx | | MG.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | system_em.gro | | topol.top | | | +---21 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---22 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---23 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---24 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---25 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---26 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---27 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---28 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---29 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---30 | helicity.dat | md.tpr | npt.tpr | nvt.tpr | rmsd_noIa_bb.xvg | rmsf.xvg | +---Metadynamics | \---Metadynamics | +---eq_after_metad | | | npt_step1.mdp | | | npt_step2.mdp | | | npt_step3.mdp | | | nvt.mdp | | | production_md.mdp | | | step6.0_minimization.mdp | | | | | +---s2_bf20_r1_fr140-72ns | | | | ATP.itp | | | | frame_140-72ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s2_bf20_r1_fr65-84ns | | | | ATP.itp | | | | frame_65-84ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s2_bf20_r1_fr85-60ns | | | | ATP.itp | | | | frame85-6ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00483.dat | | | 00484.dat | | | 00485.dat | | | | | +---s2_bf30_r1_fr115-84ns | | | | ATP.itp | | | | frame_115-84ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s2_bf30_r1_fr59-88ns | | | | ATP.itp | | | | frame_59-88ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s2_bf30_r1_fr71-36ns | | | | ATP.itp | | | | frame_71-36ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s2_bf30_r1_fr88-52ns | | | | ATP.itp | | | | frame_88-52ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf20_r1_fr38-64ns | | | | ATP.itp | | | | frame_38-64ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf25_r2_fr212-12ns | | | | ATP.itp | | | | frame_212-12ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf25_r2_fr59-36ns | | | | ATP.itp | | | | frame_59-36ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf25_r3_fr13-40ns | | | | ATP.itp | | | | frame_13-40ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf25_r3_fr29-12ns | | | | ATP.itp | | | | frame_29-12ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r1_fr11-68ns | | | | ATP.itp | | | | frame_11-68ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r1_fr21-68ns | | | | ATP.itp | | | | frame_21-68ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r1_fr24-32ns | | | | ATP.itp | | | | frame_24-32ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r1_fr8-64ns | | | | ATP.itp | | | | frame_8-64ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r2_fr255-48ns | | | | ATP.itp | | | | frame_255-48ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r2_fr429-72ns | | | | ATP.itp | | | | frame_429-72ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r3_fr172-68ns | | | | ATP.itp | | | | frame_172-68ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r3_fr26-36ns | | | | ATP.itp | | | | frame_26-36ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r4_fr29-60ns | | | | ATP.itp | | | | frame_29-60ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | +---s3_bf30_r5_fr374-88ns | | | | ATP.itp | | | | frame_374-88ns.gro | | | | md.tpr | | | | posre_ATP.itp | | | | posre_protein.itp | | | | protein.itp | | | | system_em.tpr | | | | topol.top | | | | | | | \---ConAn | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 00498.dat | | | 00499.dat | | | 00500.dat | | | | | \---s3_bf30_r5_fr49-04ns | | | ATP.itp | | | frame_49-04ns.gro | | | md.tpr | | | posre_ATP.itp | | | posre_protein.itp | | | protein.itp | | | system_em.tpr | | | topol.top | | | | | \---ConAn | | 00000.dat | | 00001.dat | | 00002.dat | | 00003.dat | | ... | | 00498.dat | | 00499.dat | | 00500.dat | | | \---metad | | Abl_ref.pdb | | Abl_start-frame.pdb | | | +---s2 | | +---bf100 | | | COLVAR | | | HILLS | | | KD-SH2_dist.xvg | | | md.tpr | | | plumed.dat | | | | | +---bf20 | | | COLVAR | | | HILLS | | | KD-SH2_dist.xvg | | | md.tpr | | | plumed.dat | | | | | +---bf30 | | | COLVAR | | | HILLS | | | KD-SH2_dist.xvg | | | md.tpr | | | plumed.dat | | | | | \---bf60 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | plumed.dat | | | \---s3 | +---bf20 | | | plumed.dat | | | | | +---1 | | | COLVAR | | | HILLS | | | KD-SH2_dist.xvg | | | md.tpr | | | | | \---2 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | | +---bf25 | | | plumed.dat | | | | | +---1 | | | COLVAR | | | HILLS | | | KD-SH2_dist.xvg | | | md.tpr | | | | | +---2 | | | COLVAR | | | HILLS | | | KD-SH2_dist.xvg | | | md.tpr | | | | | \---3 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | | \---bf30 | | plumed.dat | | | +---1 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | | +---2 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | | +---3 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | | +---4 | | COLVAR | | HILLS | | KD-SH2_dist.xvg | | md.tpr | | | \---5 | COLVAR | HILLS | KD-SH2_dist.xvg | md.tpr | +---PCA | \---PCA | autocorrelation.svg | average.pdb | bb-traj_combined.xtc | covar.log | eigenval.xvg | eigenvec.trr | extreme_active_11.pdb | extreme_active_12.pdb | extreme_active_13.pdb | extreme_active_14.pdb | extreme_active_15.pdb | extreme_active_16.pdb | extreme_active_17.pdb | extreme_active_18.pdb | extreme_active_19.pdb | extreme_active_20.pdb | extreme_active_21.pdb | extreme_active_22.pdb | extreme_active_23.pdb | extreme_active_24.pdb | extreme_active_25.pdb | extreme_active_26.pdb | extreme_active_27.pdb | extreme_active_28.pdb | extreme_active_29.pdb | extreme_active_30.pdb | extreme_kinked_Myr_11.pdb | extreme_kinked_Myr_12.pdb | extreme_kinked_Myr_13.pdb | extreme_kinked_Myr_14.pdb | extreme_kinked_Myr_15.pdb | extreme_kinked_Myr_16.pdb | extreme_kinked_Myr_17.pdb | extreme_kinked_Myr_18.pdb | extreme_kinked_Myr_19.pdb | extreme_kinked_Myr_20.pdb | extreme_kinked_Myr_21.pdb | extreme_kinked_Myr_22.pdb | extreme_kinked_Myr_23.pdb | extreme_kinked_Myr_24.pdb | extreme_kinked_Myr_25.pdb | extreme_kinked_Myr_26.pdb | extreme_kinked_Myr_27.pdb | extreme_kinked_Myr_28.pdb | extreme_kinked_Myr_29.pdb | extreme_kinked_Myr_30.pdb | extreme_kinked_noMyr_11.pdb | extreme_kinked_noMyr_12.pdb | extreme_kinked_noMyr_13.pdb | extreme_kinked_noMyr_14.pdb | extreme_kinked_noMyr_15.pdb | extreme_kinked_noMyr_16.pdb | extreme_kinked_noMyr_17.pdb | extreme_kinked_noMyr_18.pdb | extreme_kinked_noMyr_19.pdb | extreme_kinked_noMyr_20.pdb | extreme_kinked_noMyr_21.pdb | extreme_kinked_noMyr_22.pdb | extreme_kinked_noMyr_23.pdb | extreme_kinked_noMyr_24.pdb | extreme_kinked_noMyr_25.pdb | extreme_kinked_noMyr_26.pdb | extreme_kinked_noMyr_27.pdb | extreme_kinked_noMyr_28.pdb | extreme_kinked_noMyr_29.pdb | extreme_kinked_noMyr_30.pdb | extreme_straight_Myr_11.pdb | extreme_straight_Myr_12.pdb | extreme_straight_Myr_13.pdb | extreme_straight_Myr_14.pdb | extreme_straight_Myr_15.pdb | extreme_straight_Myr_16.pdb | extreme_straight_Myr_17.pdb | extreme_straight_Myr_18.pdb | extreme_straight_Myr_19.pdb | extreme_straight_Myr_20.pdb | extreme_straight_Myr_21.pdb | extreme_straight_Myr_22.pdb | extreme_straight_Myr_23.pdb | extreme_straight_Myr_24.pdb | extreme_straight_Myr_25.pdb | extreme_straight_Myr_26.pdb | extreme_straight_Myr_27.pdb | extreme_straight_Myr_28.pdb | extreme_straight_Myr_29.pdb | extreme_straight_Myr_30.pdb | extreme_straight_noMyr_11.pdb | extreme_straight_noMyr_12.pdb | extreme_straight_noMyr_13.pdb | extreme_straight_noMyr_14.pdb | extreme_straight_noMyr_15.pdb | extreme_straight_noMyr_16.pdb | extreme_straight_noMyr_17.pdb | extreme_straight_noMyr_18.pdb | extreme_straight_noMyr_19.pdb | extreme_straight_noMyr_20.pdb | extreme_straight_noMyr_21.pdb | extreme_straight_noMyr_22.pdb | extreme_straight_noMyr_23.pdb | extreme_straight_noMyr_24.pdb | extreme_straight_noMyr_25.pdb | extreme_straight_noMyr_26.pdb | extreme_straight_noMyr_27.pdb | extreme_straight_noMyr_28.pdb | extreme_straight_noMyr_29.pdb | extreme_straight_noMyr_30.pdb | extreme_whole_Myr_11.pdb | extreme_whole_Myr_12.pdb | extreme_whole_Myr_13.pdb | extreme_whole_Myr_14.pdb | extreme_whole_Myr_15.pdb | extreme_whole_Myr_16.pdb | extreme_whole_Myr_17.pdb | extreme_whole_Myr_18.pdb | extreme_whole_Myr_19.pdb | extreme_whole_Myr_20.pdb | extreme_whole_Myr_21.pdb | extreme_whole_Myr_22.pdb | extreme_whole_Myr_23.pdb | extreme_whole_Myr_24.pdb | extreme_whole_Myr_25.pdb | extreme_whole_Myr_26.pdb | extreme_whole_Myr_27.pdb | extreme_whole_Myr_28.pdb | extreme_whole_Myr_29.pdb | extreme_whole_Myr_30.pdb | extreme_whole_noMyr_11.pdb | extreme_whole_noMyr_12.pdb | extreme_whole_noMyr_13.pdb | extreme_whole_noMyr_14.pdb | extreme_whole_noMyr_15.pdb | extreme_whole_noMyr_16.pdb | extreme_whole_noMyr_17.pdb | extreme_whole_noMyr_18.pdb | extreme_whole_noMyr_19.pdb | extreme_whole_noMyr_20.pdb | extreme_whole_noMyr_21.pdb | extreme_whole_noMyr_22.pdb | extreme_whole_noMyr_23.pdb | extreme_whole_noMyr_24.pdb | extreme_whole_noMyr_25.pdb | extreme_whole_noMyr_26.pdb | extreme_whole_noMyr_27.pdb | extreme_whole_noMyr_28.pdb | extreme_whole_noMyr_29.pdb | extreme_whole_noMyr_30.pdb | KD_noIa_bb_ref.pdb | modevectors_active-kinked_extreme.pse | PCA_KDdyn_PC1-3.svg | PCA_KDdyn_PC1.svg | PCA_KDdyn_PC1_1av.csv | PCA_KDdyn_PC1_1av.svg | PCA_KDdyn_PC1_ex100av400.csv | PCA_KDdyn_PC1_ex100av400.svg | PCA_KDdyn_Pvals.csv | porcupine_active-kinked.png | porcupine_active.png | porcupine_kinked.png | proj.xvg | proj_active_11.xvg | proj_active_12.xvg | proj_active_13.xvg | proj_active_14.xvg | proj_active_15.xvg | proj_active_16.xvg | proj_active_17.xvg | proj_active_18.xvg | proj_active_19.xvg | proj_active_20.xvg | proj_active_21.xvg | proj_active_22.xvg | proj_active_23.xvg | proj_active_24.xvg | proj_active_25.xvg | proj_active_26.xvg | proj_active_27.xvg | proj_active_28.xvg | proj_active_29.xvg | proj_active_30.xvg | proj_kinked_Myr_11.xvg | proj_kinked_Myr_12.xvg | proj_kinked_Myr_13.xvg | proj_kinked_Myr_14.xvg | proj_kinked_Myr_15.xvg | proj_kinked_Myr_16.xvg | proj_kinked_Myr_17.xvg | proj_kinked_Myr_18.xvg | proj_kinked_Myr_19.xvg | proj_kinked_Myr_20.xvg | proj_kinked_Myr_21.xvg | proj_kinked_Myr_22.xvg | proj_kinked_Myr_23.xvg | proj_kinked_Myr_24.xvg | proj_kinked_Myr_25.xvg | proj_kinked_Myr_26.xvg | proj_kinked_Myr_27.xvg | proj_kinked_Myr_28.xvg | proj_kinked_Myr_29.xvg | proj_kinked_Myr_30.xvg | proj_kinked_noMyr_11.xvg | proj_kinked_noMyr_12.xvg | proj_kinked_noMyr_13.xvg | proj_kinked_noMyr_14.xvg | proj_kinked_noMyr_15.xvg | proj_kinked_noMyr_16.xvg | proj_kinked_noMyr_17.xvg | proj_kinked_noMyr_18.xvg | proj_kinked_noMyr_19.xvg | proj_kinked_noMyr_20.xvg | proj_kinked_noMyr_21.xvg | proj_kinked_noMyr_22.xvg | proj_kinked_noMyr_23.xvg | proj_kinked_noMyr_24.xvg | proj_kinked_noMyr_25.xvg | proj_kinked_noMyr_26.xvg | proj_kinked_noMyr_27.xvg | proj_kinked_noMyr_28.xvg | proj_kinked_noMyr_29.xvg | proj_kinked_noMyr_30.xvg | proj_straight_Myr_11.xvg | proj_straight_Myr_12.xvg | proj_straight_Myr_13.xvg | proj_straight_Myr_14.xvg | proj_straight_Myr_15.xvg | proj_straight_Myr_16.xvg | proj_straight_Myr_17.xvg | proj_straight_Myr_18.xvg | proj_straight_Myr_19.xvg | proj_straight_Myr_20.xvg | proj_straight_Myr_21.xvg | proj_straight_Myr_22.xvg | proj_straight_Myr_23.xvg | proj_straight_Myr_24.xvg | proj_straight_Myr_25.xvg | proj_straight_Myr_26.xvg | proj_straight_Myr_27.xvg | proj_straight_Myr_28.xvg | proj_straight_Myr_29.xvg | proj_straight_Myr_30.xvg | proj_straight_noMyr_11.xvg | proj_straight_noMyr_12.xvg | proj_straight_noMyr_13.xvg | proj_straight_noMyr_14.xvg | proj_straight_noMyr_15.xvg | proj_straight_noMyr_16.xvg | proj_straight_noMyr_17.xvg | proj_straight_noMyr_18.xvg | proj_straight_noMyr_19.xvg | proj_straight_noMyr_20.xvg | proj_straight_noMyr_21.xvg | proj_straight_noMyr_22.xvg | proj_straight_noMyr_23.xvg | proj_straight_noMyr_24.xvg | proj_straight_noMyr_25.xvg | proj_straight_noMyr_26.xvg | proj_straight_noMyr_27.xvg | proj_straight_noMyr_28.xvg | proj_straight_noMyr_29.xvg | proj_straight_noMyr_30.xvg | proj_whole_Myr_11.xvg | proj_whole_Myr_12.xvg | proj_whole_Myr_13.xvg | proj_whole_Myr_14.xvg | proj_whole_Myr_15.xvg | proj_whole_Myr_16.xvg | proj_whole_Myr_17.xvg | proj_whole_Myr_18.xvg | proj_whole_Myr_19.xvg | proj_whole_Myr_20.xvg | proj_whole_Myr_21.xvg | proj_whole_Myr_22.xvg | proj_whole_Myr_23.xvg | proj_whole_Myr_24.xvg | proj_whole_Myr_25.xvg | proj_whole_Myr_26.xvg | proj_whole_Myr_27.xvg | proj_whole_Myr_28.xvg | proj_whole_Myr_29.xvg | proj_whole_Myr_30.xvg | proj_whole_noMyr_11.xvg | proj_whole_noMyr_12.xvg | proj_whole_noMyr_13.xvg | proj_whole_noMyr_14.xvg | proj_whole_noMyr_15.xvg | proj_whole_noMyr_16.xvg | proj_whole_noMyr_17.xvg | proj_whole_noMyr_18.xvg | proj_whole_noMyr_19.xvg | proj_whole_noMyr_20.xvg | proj_whole_noMyr_21.xvg | proj_whole_noMyr_22.xvg | proj_whole_noMyr_23.xvg | proj_whole_noMyr_24.xvg | proj_whole_noMyr_25.xvg | proj_whole_noMyr_26.xvg | proj_whole_noMyr_27.xvg | proj_whole_noMyr_28.xvg | proj_whole_noMyr_29.xvg | proj_whole_noMyr_30.xvg | steps | traj_active_11.xtc | traj_active_12.xtc | traj_active_13.xtc | traj_active_14.xtc | traj_active_15.xtc | traj_active_16.xtc | traj_active_17.xtc | traj_active_18.xtc | traj_active_19.xtc | traj_active_20.xtc | traj_active_21.xtc | traj_active_22.xtc | traj_active_23.xtc | traj_active_24.xtc | traj_active_25.xtc | traj_active_26.xtc | traj_active_27.xtc | traj_active_28.xtc | traj_active_29.xtc | traj_active_30.xtc | traj_kinked_Myr_11.xtc | traj_kinked_Myr_12.xtc | traj_kinked_Myr_13.xtc | traj_kinked_Myr_14.xtc | traj_kinked_Myr_15.xtc | traj_kinked_Myr_16.xtc | traj_kinked_Myr_17.xtc | traj_kinked_Myr_18.xtc | traj_kinked_Myr_19.xtc | traj_kinked_Myr_20.xtc | traj_kinked_Myr_21.xtc | traj_kinked_Myr_22.xtc | traj_kinked_Myr_23.xtc | traj_kinked_Myr_24.xtc | traj_kinked_Myr_25.xtc | traj_kinked_Myr_26.xtc | traj_kinked_Myr_27.xtc | traj_kinked_Myr_28.xtc | traj_kinked_Myr_29.xtc | traj_kinked_Myr_30.xtc | traj_kinked_noMyr_11.xtc | traj_kinked_noMyr_12.xtc | traj_kinked_noMyr_13.xtc | traj_kinked_noMyr_14.xtc | traj_kinked_noMyr_15.xtc | traj_kinked_noMyr_16.xtc | traj_kinked_noMyr_17.xtc | traj_kinked_noMyr_18.xtc | traj_kinked_noMyr_19.xtc | traj_kinked_noMyr_20.xtc | traj_kinked_noMyr_21.xtc | traj_kinked_noMyr_22.xtc | traj_kinked_noMyr_23.xtc | traj_kinked_noMyr_24.xtc | traj_kinked_noMyr_25.xtc | traj_kinked_noMyr_26.xtc | traj_kinked_noMyr_27.xtc | traj_kinked_noMyr_28.xtc | traj_kinked_noMyr_29.xtc | traj_kinked_noMyr_30.xtc | traj_straight_Myr_11.xtc | traj_straight_Myr_12.xtc | traj_straight_Myr_13.xtc | traj_straight_Myr_14.xtc | traj_straight_Myr_15.xtc | traj_straight_Myr_16.xtc | traj_straight_Myr_17.xtc | traj_straight_Myr_18.xtc | traj_straight_Myr_19.xtc | traj_straight_Myr_20.xtc | traj_straight_Myr_21.xtc | traj_straight_Myr_22.xtc | traj_straight_Myr_23.xtc | traj_straight_Myr_24.xtc | traj_straight_Myr_25.xtc | traj_straight_Myr_26.xtc | traj_straight_Myr_27.xtc | traj_straight_Myr_28.xtc | traj_straight_Myr_29.xtc | traj_straight_Myr_30.xtc | traj_straight_noMyr_11.xtc | traj_straight_noMyr_12.xtc | traj_straight_noMyr_13.xtc | traj_straight_noMyr_14.xtc | traj_straight_noMyr_15.xtc | traj_straight_noMyr_16.xtc | traj_straight_noMyr_17.xtc | traj_straight_noMyr_18.xtc | traj_straight_noMyr_19.xtc | traj_straight_noMyr_20.xtc | traj_straight_noMyr_21.xtc | traj_straight_noMyr_22.xtc | traj_straight_noMyr_23.xtc | traj_straight_noMyr_24.xtc | traj_straight_noMyr_25.xtc | traj_straight_noMyr_26.xtc | traj_straight_noMyr_27.xtc | traj_straight_noMyr_28.xtc | traj_straight_noMyr_29.xtc | traj_straight_noMyr_30.xtc | traj_whole_Myr_11.xtc | traj_whole_Myr_12.xtc | traj_whole_Myr_13.xtc | traj_whole_Myr_14.xtc | traj_whole_Myr_15.xtc | traj_whole_Myr_16.xtc | traj_whole_Myr_17.xtc | traj_whole_Myr_18.xtc | traj_whole_Myr_19.xtc | traj_whole_Myr_20.xtc | traj_whole_Myr_21.xtc | traj_whole_Myr_22.xtc | traj_whole_Myr_23.xtc | traj_whole_Myr_24.xtc | traj_whole_Myr_25.xtc | traj_whole_Myr_26.xtc | traj_whole_Myr_27.xtc | traj_whole_Myr_28.xtc | traj_whole_Myr_29.xtc | traj_whole_Myr_30.xtc | traj_whole_noMyr_11.xtc | traj_whole_noMyr_12.xtc | traj_whole_noMyr_13.xtc | traj_whole_noMyr_14.xtc | traj_whole_noMyr_15.xtc | traj_whole_noMyr_16.xtc | traj_whole_noMyr_17.xtc | traj_whole_noMyr_18.xtc | traj_whole_noMyr_19.xtc | traj_whole_noMyr_20.xtc | traj_whole_noMyr_21.xtc | traj_whole_noMyr_22.xtc | traj_whole_noMyr_23.xtc | traj_whole_noMyr_24.xtc | traj_whole_noMyr_25.xtc | traj_whole_noMyr_26.xtc | traj_whole_noMyr_27.xtc | traj_whole_noMyr_28.xtc | traj_whole_noMyr_29.xtc | traj_whole_noMyr_30.xtc | +---setup_analysis | analysis_Fig1-B-E.sh | eq_sim_setup_steps.txt | +---SH3-SH2-KD_Myr | \---SH3-SH2-KD_Myr | +---Set1 | | | ATP.itp | | | index.ndx | | | MG.itp | | | MYR.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_MYR.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---12 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---13 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---14 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---15 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---16 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---17 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---18 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---19 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | \---20 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---Set2 | | ATP.itp | | index.ndx | | MG.itp | | MYR.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_MYR.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | system_em.gro | | topol.top | | | +---21 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---22 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---23 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---24 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---25 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---26 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---27 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---28 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---29 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---30 | helicity.dat | md.tpr | npt.tpr | nvt.tpr | rmsd_noIa_bb.xvg | rmsf.xvg | +---SH3-SH2-KD_noMyr | \---SH3-SH2-KD_noMyr | +---ConAn | | | SH2-KD_av_contacts_reps.csv | | | SH2-KD_contacts_native.csv | | | SH2-KD_median_contacts_time.csv | | | | | +---1 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---10 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---2 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---3 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---4 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---5 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---6 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---7 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | +---8 | | | 00000.dat | | | 00001.dat | | | 00002.dat | | | 00003.dat | | | ... | | | 02498.dat | | | 02499.dat | | | 02500.dat | | | KD-SH2_dist.xvg | | | | | \---9 | | 00000.dat | | 00001.dat | | 00002.dat | | 00003.dat | | ... | | 02498.dat | | 02499.dat | | 02500.dat | | KD-SH2_dist.xvg | | | +---Set1 | | | ATP.itp | | | index.ndx | | | MG.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_MG.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.itp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_solv.gro | | | system_solv_ions.gro | | | topol.top | | | | | +---11 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---12 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---13 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---14 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---15 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---16 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---17 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---18 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | +---19 | | | helicity.dat | | | md.tpr | | | npt.tpr | | | nvt.tpr | | | rmsd_noIa_bb.xvg | | | rmsf.xvg | | | | | \---20 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---Set2 | | ATP.itp | | index.ndx | | MG.itp | | npt.mdp | | nvt.mdp | | posre_ATP.itp | | posre_MG.itp | | posre_protein.itp | | production_md.mdp | | protein.itp | | system_em.gro | | topol.top | | | +---21 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---22 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---23 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---24 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---25 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---26 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---27 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---28 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | +---29 | | helicity.dat | | md.tpr | | npt.tpr | | nvt.tpr | | rmsd_noIa_bb.xvg | | rmsf.xvg | | | \---30 | helicity.dat | md.tpr | npt.tpr | nvt.tpr | rmsd_noIa_bb.xvg | rmsf.xvg | \---Umbrella \---Umbrella | Abl_Myr_pull_setup | analyze_umbrella.sh | start_umbrella.sh | umbrella_md.mdp | umbrella_npt.mdp | umbrella_sampling_steps | umbrella_submit.sh | +---alphaI-kink | +---eq | | | ATP.gro | | | ATP.itp | | | GLYM.gro | | | GLYM.itp | | | ionize.tpr | | | mdout.mdp | | | MG.gro | | | npt.gro | | | npt.mdp | | | npt.tpr | | | npt_prot.gro | | | nvt.gro | | | nvt.mdp | | | nvt.tpr | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | protein.gro | | | protein.itp | | | step6.0_minimization.mdp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_em.tpr | | | system_solv.gro | | | system_solv_ions.gro | | | topol_sys.top | | | | | +---1 | | | md.tpr | | | | | +---10 | | | md.tpr | | | | | +---2 | | | md.tpr | | | | | +---3 | | | md.tpr | | | | | +---4 | | | md.tpr | | | | | +---5 | | | md.tpr | | | | | +---6 | | | md.tpr | | | | | +---7 | | | md.tpr | | | | | +---8 | | | md.tpr | | | | | \---9 | | md.tpr | | | +---pull | | | ATP.itp | | | GLYM.itp | | | mdout.mdp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | protein.itp | | | pull_md.mdp | | | step6.0_minimization.mdp | | | topol.top | | | | | +---1 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---2 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.1ms.tpr | | | | | +---3 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---5 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---6 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---7 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | \---8 | | eq_md.gro | | npt.tpr | | nvt.tpr | | pull_em.tpr | | pull_md_0.05ms.tpr | | pull_md_0.1ms.tpr | | | \---umbrella | 1_05_165.tpr | 1_05_165_pullx.xvg | 1_05_202.tpr | 1_05_202_pullx.xvg | 1_05_25.tpr | 1_05_25_pullx.xvg | 1_05_322.tpr | 1_05_322_pullx.xvg | 1_05_359.tpr | 1_05_359_pullx.xvg | 1_05_463.tpr | 1_05_463_pullx.xvg | 1_05_50.tpr | 1_05_50_pullx.xvg | 1_05_555.tpr | 1_05_555_pullx.xvg | 1_05_573.tpr | 1_05_573_pullx.xvg | 1_05_591.tpr | 1_05_591_pullx.xvg | 1_05_675.tpr | 1_05_675_pullx.xvg | 1_05_687.tpr | 1_05_687_pullx.xvg | 1_05_71.tpr | 1_05_71_pullx.xvg | 1_05_730.tpr | 1_05_730_pullx.xvg | 1_05_750.tpr | 1_05_750_pullx.xvg | 1_05_831.tpr | 1_05_831_pullx.xvg | 1_05_897.tpr | 1_05_897_pullx.xvg | 1_05_924.tpr | 1_05_924_pullx.xvg | 1_1_1.tpr | 1_1_132.tpr | 1_1_132_pullx.xvg | 1_1_1_pullx.xvg | 1_1_20.tpr | 1_1_20_pullx.xvg | 1_1_221.tpr | 1_1_221_pullx.xvg | 1_1_255.tpr | 1_1_255_pullx.xvg | 1_1_282.tpr | 1_1_282_pullx.xvg | 1_1_288.tpr | 1_1_288_pullx.xvg | 1_1_294.tpr | 1_1_294_pullx.xvg | 1_1_371.tpr | 1_1_371_pullx.xvg | 1_1_403.tpr | 1_1_403_pullx.xvg | 1_1_437.tpr | 1_1_437_pullx.xvg | 1_1_508.tpr | 1_1_508_pullx.xvg | 1_1_523.tpr | 1_1_523_pullx.xvg | 1_1_568.tpr | 1_1_568_pullx.xvg | 1_1_582.tpr | 1_1_582_pullx.xvg | 1_1_590.tpr | 1_1_590_pullx.xvg | 1_1_592.tpr | 1_1_592_pullx.xvg | 1_1_602.tpr | 1_1_602_pullx.xvg | 1_1_91.tpr | 1_1_91_pullx.xvg | 3_05_1028.tpr | 3_05_1028_pullx.xvg | 3_05_1085.tpr | 3_05_1085_pullx.xvg | 3_05_112.tpr | 3_05_112_pullx.xvg | 3_05_1189.tpr | 3_05_1189_pullx.xvg | 3_05_1210.tpr | 3_05_1210_pullx.xvg | 3_05_1336.tpr | 3_05_1336_pullx.xvg | 3_05_1444.tpr | 3_05_1444_pullx.xvg | 3_05_1477.tpr | 3_05_1477_pullx.xvg | 3_05_1544.tpr | 3_05_1544_pullx.xvg | 3_05_220.tpr | 3_05_220_pullx.xvg | 3_05_223.tpr | 3_05_223_pullx.xvg | 3_05_243.tpr | 3_05_243_pullx.xvg | 3_05_278.tpr | 3_05_278_pullx.xvg | 3_05_292.tpr | 3_05_292_pullx.xvg | 3_05_407.tpr | 3_05_407_pullx.xvg | 3_05_499.tpr | 3_05_499_pullx.xvg | 3_05_592.tpr | 3_05_592_pullx.xvg | 3_05_68.tpr | 3_05_68_pullx.xvg | 3_05_697.tpr | 3_05_697_pullx.xvg | 3_05_903.tpr | 3_05_903_pullx.xvg | 3_05_93.tpr | 3_05_93_pullx.xvg | 3_1_12.tpr | 3_1_124.tpr | 3_1_124_pullx.xvg | 3_1_12_pullx.xvg | 3_1_152.tpr | 3_1_152_pullx.xvg | 3_1_192.tpr | 3_1_192_pullx.xvg | 3_1_201.tpr | 3_1_201_pullx.xvg | 3_1_216.tpr | 3_1_216_pullx.xvg | 3_1_26.tpr | 3_1_26_pullx.xvg | 3_1_279.tpr | 3_1_279_pullx.xvg | 3_1_288.tpr | 3_1_288_pullx.xvg | 3_1_425.tpr | 3_1_425_pullx.xvg | 3_1_469.tpr | 3_1_469_pullx.xvg | 3_1_511.tpr | 3_1_511_pullx.xvg | 3_1_544.tpr | 3_1_544_pullx.xvg | 3_1_574.tpr | 3_1_574_pullx.xvg | 3_1_635.tpr | 3_1_635_pullx.xvg | 3_1_667.tpr | 3_1_667_pullx.xvg | 3_1_70.tpr | 3_1_701.tpr | 3_1_701_pullx.xvg | 3_1_70_pullx.xvg | 3_1_713.tpr | 3_1_713_pullx.xvg | 5_05_1015.tpr | 5_05_1015_pullx.xvg | 5_05_1084.tpr | 5_05_1084_pullx.xvg | 5_05_1093.tpr | 5_05_1093_pullx.xvg | 5_05_12.tpr | 5_05_1275.tpr | 5_05_1275_pullx.xvg | 5_05_12_pullx.xvg | 5_05_204.tpr | 5_05_204_pullx.xvg | 5_05_249.tpr | 5_05_249_pullx.xvg | 5_05_305.tpr | 5_05_305_pullx.xvg | 5_05_364.tpr | 5_05_364_pullx.xvg | 5_05_374.tpr | 5_05_374_pullx.xvg | 5_05_409.tpr | 5_05_409_pullx.xvg | 5_05_543.tpr | 5_05_543_pullx.xvg | 5_05_58.tpr | 5_05_58_pullx.xvg | 5_05_60.tpr | 5_05_603.tpr | 5_05_603_pullx.xvg | 5_05_60_pullx.xvg | 5_05_719.tpr | 5_05_719_pullx.xvg | 5_05_8.tpr | 5_05_801.tpr | 5_05_801_pullx.xvg | 5_05_8_pullx.xvg | 5_05_932.tpr | 5_05_932_pullx.xvg | 5_1_10.tpr | 5_1_104.tpr | 5_1_104_pullx.xvg | 5_1_10_pullx.xvg | 5_1_12.tpr | 5_1_12_pullx.xvg | 5_1_168.tpr | 5_1_168_pullx.xvg | 5_1_184.tpr | 5_1_184_pullx.xvg | 5_1_20.tpr | 5_1_20_pullx.xvg | 5_1_248.tpr | 5_1_248_pullx.xvg | 5_1_272.tpr | 5_1_272_pullx.xvg | 5_1_318.tpr | 5_1_318_pullx.xvg | 5_1_378.tpr | 5_1_378_pullx.xvg | 5_1_415.tpr | 5_1_415_pullx.xvg | 5_1_437.tpr | 5_1_437_pullx.xvg | 5_1_486.tpr | 5_1_486_pullx.xvg | 5_1_537.tpr | 5_1_537_pullx.xvg | 5_1_583.tpr | 5_1_583_pullx.xvg | 5_1_628.tpr | 5_1_628_pullx.xvg | 5_1_64.tpr | 5_1_64_pullx.xvg | 5_1_82.tpr | 5_1_82_pullx.xvg | analyze_umbrella_blocks.sh | analyze_umbrella_final.sh | bsProfs_100-120ns.xvg | bsProfs_120-140ns.xvg | bsProfs_140-160ns.xvg | bsProfs_160-180ns.xvg | bsProfs_180-200ns.xvg | bsProfs_20-40ns.xvg | bsProfs_40-60ns.xvg | bsProfs_60-80ns.xvg | bsProfs_80-100ns.xvg | bsProfs_80-200ns.xvg | bsResult_100-120ns.xvg | bsResult_120-140ns.xvg | bsResult_140-160ns.xvg | bsResult_160-180ns.xvg | bsResult_180-200ns.xvg | bsResult_20-40ns.xvg | bsResult_40-60ns.xvg | bsResult_60-80ns.xvg | bsResult_80-100ns.xvg | bsResult_80-200ns.xvg | frames.dat | histo_100-120ns.xvg | histo_120-140ns.xvg | histo_140-160ns.xvg | histo_160-180ns.xvg | histo_180-200ns.xvg | histo_20-40ns.xvg | histo_40-60ns.xvg | histo_60-80ns.xvg | histo_80-100ns.xvg | histo_80-200ns.xvg | profile_100-120ns.xvg | profile_120-140ns.xvg | profile_140-160ns.xvg | profile_160-180ns.xvg | profile_180-200ns.xvg | profile_20-40ns.xvg | profile_40-60ns.xvg | profile_60-80ns.xvg | profile_80-100ns.xvg | profile_80-200ns.xvg | pullx_files.dat | tpr_files.dat | +---alphaI-straight | +---eq | | | ATP.gro | | | ATP.itp | | | GLYM.gro | | | GLYM.itp | | | ionize.tpr | | | md.tpr | | | mdout.mdp | | | MG.gro | | | npt.gro | | | npt.mdp | | | npt.tpr | | | nvt.gro | | | nvt.mdp | | | nvt.tpr | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.gro | | | protein.itp | | | step6.0_minimization.mdp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_em.tpr | | | system_solv.gro | | | system_solv_ions.gro | | | topol_sys.top | | | | | +---1 | | | md.tpr | | | | | +---10 | | | md.tpr | | | | | +---2 | | | md.tpr | | | | | +---3 | | | md.tpr | | | | | +---4 | | | md.tpr | | | | | +---5 | | | md.tpr | | | | | +---6 | | | md.tpr | | | | | +---7 | | | md.tpr | | | | | +---8 | | | md.tpr | | | | | \---9 | | md.tpr | | | +---pull | | | ATP.itp | | | GLYM.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | protein.itp | | | pull_md.mdp | | | step6.0_minimization.mdp | | | topol.top | | | | | +---1 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---10 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---2 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---3 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---4 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---5 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---6 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---8 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | \---9 | | eq_md.gro | | npt.tpr | | nvt.tpr | | pull_em.tpr | | pull_md_0.05ms.tpr | | pull_md_0.1ms.tpr | | | \---umbrella | 1_05_1011.tpr | 1_05_1011_pullx.xvg | 1_05_110.tpr | 1_05_1107.tpr | 1_05_1107_pullx.xvg | 1_05_110_pullx.xvg | 1_05_1224.tpr | 1_05_1224_pullx.xvg | 1_05_1250.tpr | 1_05_1250_pullx.xvg | 1_05_1292.tpr | 1_05_1292_pullx.xvg | 1_05_1318.tpr | 1_05_1318_pullx.xvg | 1_05_1355.tpr | 1_05_1355_pullx.xvg | 1_05_1371.tpr | 1_05_1371_pullx.xvg | 1_05_1439.tpr | 1_05_1439_pullx.xvg | 1_05_1727.tpr | 1_05_1727_pullx.xvg | 1_05_173.tpr | 1_05_173_pullx.xvg | 1_05_1768.tpr | 1_05_1768_pullx.xvg | 1_05_1814.tpr | 1_05_1814_pullx.xvg | 1_05_1847.tpr | 1_05_1847_pullx.xvg | 1_05_205.tpr | 1_05_205_pullx.xvg | 1_05_251.tpr | 1_05_251_pullx.xvg | 1_05_254.tpr | 1_05_254_pullx.xvg | 1_05_288.tpr | 1_05_288_pullx.xvg | 1_05_309.tpr | 1_05_309_pullx.xvg | 1_05_463.tpr | 1_05_463_pullx.xvg | 1_05_73.tpr | 1_05_73_pullx.xvg | 1_05_918.tpr | 1_05_918_pullx.xvg | 1_05_978.tpr | 1_05_978_pullx.xvg | 1_05_99.tpr | 1_05_99_pullx.xvg | 1_1_134.tpr | 1_1_134_pullx.xvg | 1_1_203.tpr | 1_1_203_pullx.xvg | 1_1_234.tpr | 1_1_234_pullx.xvg | 1_1_302.tpr | 1_1_302_pullx.xvg | 1_1_376.tpr | 1_1_376_pullx.xvg | 1_1_38.tpr | 1_1_38_pullx.xvg | 1_1_41.tpr | 1_1_41_pullx.xvg | 1_1_429.tpr | 1_1_429_pullx.xvg | 1_1_461.tpr | 1_1_461_pullx.xvg | 1_1_529.tpr | 1_1_529_pullx.xvg | 1_1_558.tpr | 1_1_558_pullx.xvg | 1_1_590.tpr | 1_1_590_pullx.xvg | 1_1_627.tpr | 1_1_627_pullx.xvg | 1_1_655.tpr | 1_1_655_pullx.xvg | 1_1_735.tpr | 1_1_735_pullx.xvg | 1_1_778.tpr | 1_1_778_pullx.xvg | 1_1_812.tpr | 1_1_812_pullx.xvg | 1_1_836.tpr | 1_1_836_pullx.xvg | 1_1_885.tpr | 1_1_885_pullx.xvg | 1_1_900.tpr | 1_1_900_pullx.xvg | 1_1_92.tpr | 1_1_92_pullx.xvg | 2_05_1040.tpr | 2_05_1040_pullx.xvg | 2_05_1210.tpr | 2_05_1210_pullx.xvg | 2_05_1344.tpr | 2_05_1344_pullx.xvg | 2_05_1373.tpr | 2_05_1373_pullx.xvg | 2_05_1434.tpr | 2_05_1434_pullx.xvg | 2_05_1481.tpr | 2_05_1481_pullx.xvg | 2_05_1490.tpr | 2_05_1490_pullx.xvg | 2_05_1530.tpr | 2_05_1530_pullx.xvg | 2_05_1654.tpr | 2_05_1654_pullx.xvg | 2_05_1706.tpr | 2_05_1706_pullx.xvg | 2_05_1758.tpr | 2_05_1758_pullx.xvg | 2_05_1787.tpr | 2_05_1787_pullx.xvg | 2_05_187.tpr | 2_05_187_pullx.xvg | 2_05_1885.tpr | 2_05_1885_pullx.xvg | 2_05_191.tpr | 2_05_1915.tpr | 2_05_1915_pullx.xvg | 2_05_191_pullx.xvg | 2_05_1959.tpr | 2_05_1959_pullx.xvg | 2_05_207.tpr | 2_05_207_pullx.xvg | 2_05_2103.tpr | 2_05_2103_pullx.xvg | 2_05_245.tpr | 2_05_245_pullx.xvg | 2_05_374.tpr | 2_05_374_pullx.xvg | 2_05_424.tpr | 2_05_424_pullx.xvg | 2_05_509.tpr | 2_05_509_pullx.xvg | 2_05_573.tpr | 2_05_573_pullx.xvg | 2_05_775.tpr | 2_05_775_pullx.xvg | 2_05_905.tpr | 2_05_905_pullx.xvg | 2_1_100.tpr | 2_1_100_pullx.xvg | 2_1_105.tpr | 2_1_105_pullx.xvg | 2_1_131.tpr | 2_1_131_pullx.xvg | 2_1_156.tpr | 2_1_156_pullx.xvg | 2_1_190.tpr | 2_1_190_pullx.xvg | 2_1_266.tpr | 2_1_266_pullx.xvg | 2_1_469.tpr | 2_1_469_pullx.xvg | 2_1_512.tpr | 2_1_512_pullx.xvg | 2_1_551.tpr | 2_1_551_pullx.xvg | 2_1_584.tpr | 2_1_584_pullx.xvg | 2_1_597.tpr | 2_1_597_pullx.xvg | 2_1_633.tpr | 2_1_633_pullx.xvg | 2_1_651.tpr | 2_1_651_pullx.xvg | 2_1_679.tpr | 2_1_679_pullx.xvg | 2_1_706.tpr | 2_1_706_pullx.xvg | 2_1_714.tpr | 2_1_714_pullx.xvg | 2_1_758.tpr | 2_1_758_pullx.xvg | 2_1_768.tpr | 2_1_768_pullx.xvg | 2_1_783.tpr | 2_1_783_pullx.xvg | 2_1_837.tpr | 2_1_837_pullx.xvg | 2_1_925.tpr | 2_1_925_pullx.xvg | 2_1_927.tpr | 2_1_927_pullx.xvg | 2_1_971.tpr | 2_1_971_pullx.xvg | 2_1_994.tpr | 2_1_994_pullx.xvg | 3_05_1215.tpr | 3_05_1215_pullx.xvg | 3_05_1234.tpr | 3_05_1234_pullx.xvg | 3_05_1415.tpr | 3_05_1415_pullx.xvg | 3_05_1456.tpr | 3_05_1456_pullx.xvg | 3_05_1554.tpr | 3_05_1554_pullx.xvg | 3_05_156.tpr | 3_05_156_pullx.xvg | 3_05_162.tpr | 3_05_162_pullx.xvg | 3_05_1729.tpr | 3_05_1729_pullx.xvg | 3_05_1841.tpr | 3_05_1841_pullx.xvg | 3_05_1892.tpr | 3_05_1892_pullx.xvg | 3_05_1942.tpr | 3_05_1942_pullx.xvg | 3_05_197.tpr | 3_05_197_pullx.xvg | 3_05_2000.tpr | 3_05_2000_pullx.xvg | 3_05_2048.tpr | 3_05_2048_pullx.xvg | 3_05_2059.tpr | 3_05_2059_pullx.xvg | 3_05_2139.tpr | 3_05_2139_pullx.xvg | 3_05_2209.tpr | 3_05_2209_pullx.xvg | 3_05_2275.tpr | 3_05_2275_pullx.xvg | 3_05_243.tpr | 3_05_243_pullx.xvg | 3_05_342.tpr | 3_05_342_pullx.xvg | 3_05_360.tpr | 3_05_360_pullx.xvg | 3_05_450.tpr | 3_05_450_pullx.xvg | 3_05_596.tpr | 3_05_596_pullx.xvg | 3_05_63.tpr | 3_05_63_pullx.xvg | 3_05_719.tpr | 3_05_719_pullx.xvg | 3_05_764.tpr | 3_05_764_pullx.xvg | 3_05_922.tpr | 3_05_922_pullx.xvg | 3_1_1056.tpr | 3_1_1056_pullx.xvg | 3_1_1068.tpr | 3_1_1068_pullx.xvg | 3_1_1079.tpr | 3_1_1079_pullx.xvg | 3_1_1086.tpr | 3_1_1086_pullx.xvg | 3_1_1119.tpr | 3_1_1119_pullx.xvg | 3_1_121.tpr | 3_1_121_pullx.xvg | 3_1_183.tpr | 3_1_183_pullx.xvg | 3_1_21.tpr | 3_1_219.tpr | 3_1_219_pullx.xvg | 3_1_21_pullx.xvg | 3_1_290.tpr | 3_1_290_pullx.xvg | 3_1_315.tpr | 3_1_315_pullx.xvg | 3_1_321.tpr | 3_1_321_pullx.xvg | 3_1_334.tpr | 3_1_334_pullx.xvg | 3_1_355.tpr | 3_1_355_pullx.xvg | 3_1_382.tpr | 3_1_382_pullx.xvg | 3_1_429.tpr | 3_1_429_pullx.xvg | 3_1_530.tpr | 3_1_530_pullx.xvg | 3_1_60.tpr | 3_1_60_pullx.xvg | 3_1_670.tpr | 3_1_670_pullx.xvg | 3_1_688.tpr | 3_1_688_pullx.xvg | 3_1_703.tpr | 3_1_703_pullx.xvg | 3_1_732.tpr | 3_1_732_pullx.xvg | 3_1_780.tpr | 3_1_780_pullx.xvg | 3_1_828.tpr | 3_1_828_pullx.xvg | 3_1_901.tpr | 3_1_901_pullx.xvg | 3_1_934.tpr | 3_1_934_pullx.xvg | 3_1_968.tpr | 3_1_968_pullx.xvg | 6_05_103.tpr | 6_05_103_pullx.xvg | 6_05_1083.tpr | 6_05_1083_pullx.xvg | 6_05_1171.tpr | 6_05_1171_pullx.xvg | 6_05_1257.tpr | 6_05_1257_pullx.xvg | 6_05_1312.tpr | 6_05_1312_pullx.xvg | 6_05_1453.tpr | 6_05_1453_pullx.xvg | 6_05_1472.tpr | 6_05_1472_pullx.xvg | 6_05_156.tpr | 6_05_1565.tpr | 6_05_1565_pullx.xvg | 6_05_156_pullx.xvg | 6_05_1594.tpr | 6_05_1594_pullx.xvg | 6_05_1657.tpr | 6_05_1657_pullx.xvg | 6_05_1674.tpr | 6_05_1674_pullx.xvg | 6_05_1721.tpr | 6_05_1721_pullx.xvg | 6_05_1811.tpr | 6_05_1811_pullx.xvg | 6_05_1991.tpr | 6_05_1991_pullx.xvg | 6_05_2014.tpr | 6_05_2014_pullx.xvg | 6_05_286.tpr | 6_05_286_pullx.xvg | 6_05_305.tpr | 6_05_305_pullx.xvg | 6_05_343.tpr | 6_05_343_pullx.xvg | 6_05_388.tpr | 6_05_388_pullx.xvg | 6_05_457.tpr | 6_05_457_pullx.xvg | 6_05_589.tpr | 6_05_589_pullx.xvg | 6_05_812.tpr | 6_05_812_pullx.xvg | 6_05_838.tpr | 6_05_838_pullx.xvg | 6_05_982.tpr | 6_05_982_pullx.xvg | 6_05_998.tpr | 6_05_998_pullx.xvg | 6_1_1008.tpr | 6_1_1008_pullx.xvg | 6_1_13.tpr | 6_1_13_pullx.xvg | 6_1_169.tpr | 6_1_169_pullx.xvg | 6_1_189.tpr | 6_1_189_pullx.xvg | 6_1_266.tpr | 6_1_266_pullx.xvg | 6_1_320.tpr | 6_1_320_pullx.xvg | 6_1_402.tpr | 6_1_402_pullx.xvg | 6_1_500.tpr | 6_1_500_pullx.xvg | 6_1_57.tpr | 6_1_57_pullx.xvg | 6_1_603.tpr | 6_1_603_pullx.xvg | 6_1_619.tpr | 6_1_619_pullx.xvg | 6_1_631.tpr | 6_1_631_pullx.xvg | 6_1_710.tpr | 6_1_710_pullx.xvg | 6_1_738.tpr | 6_1_738_pullx.xvg | 6_1_745.tpr | 6_1_745_pullx.xvg | 6_1_774.tpr | 6_1_774_pullx.xvg | 6_1_839.tpr | 6_1_839_pullx.xvg | 6_1_845.tpr | 6_1_845_pullx.xvg | 6_1_894.tpr | 6_1_894_pullx.xvg | 6_1_934.tpr | 6_1_934_pullx.xvg | 6_1_95.tpr | 6_1_95_pullx.xvg | 6_1_990.tpr | 6_1_990_pullx.xvg | 6_1_998.tpr | 6_1_998_pullx.xvg | 8_05_0.tpr | 8_05_0_pullx.xvg | 8_05_1032.tpr | 8_05_1032_pullx.xvg | 8_05_1270.tpr | 8_05_1270_pullx.xvg | 8_05_1382.tpr | 8_05_1382_pullx.xvg | 8_05_1498.tpr | 8_05_1498_pullx.xvg | 8_05_1672.tpr | 8_05_1672_pullx.xvg | 8_05_1778.tpr | 8_05_1778_pullx.xvg | 8_05_1816.tpr | 8_05_1816_pullx.xvg | 8_05_1884.tpr | 8_05_1884_pullx.xvg | 8_05_1912.tpr | 8_05_1912_pullx.xvg | 8_05_1971.tpr | 8_05_1971_pullx.xvg | 8_05_198.tpr | 8_05_1983.tpr | 8_05_1983_pullx.xvg | 8_05_198_pullx.xvg | 8_05_1991.tpr | 8_05_1991_pullx.xvg | 8_05_2016.tpr | 8_05_2016_pullx.xvg | 8_05_2017.tpr | 8_05_2017_pullx.xvg | 8_05_209.tpr | 8_05_209_pullx.xvg | 8_05_2120.tpr | 8_05_2120_pullx.xvg | 8_05_2121.tpr | 8_05_2121_pullx.xvg | 8_05_2262.tpr | 8_05_2262_pullx.xvg | 8_05_2300.tpr | 8_05_2300_pullx.xvg | 8_05_2474.tpr | 8_05_2474_pullx.xvg | 8_05_269.tpr | 8_05_269_pullx.xvg | 8_05_342.tpr | 8_05_342_pullx.xvg | 8_05_38.tpr | 8_05_38_pullx.xvg | 8_05_478.tpr | 8_05_478_pullx.xvg | 8_05_626.tpr | 8_05_626_pullx.xvg | 8_05_769.tpr | 8_05_769_pullx.xvg | 8_05_78.tpr | 8_05_78_pullx.xvg | 8_05_852.tpr | 8_05_852_pullx.xvg | 8_1_0.tpr | 8_1_0_pullx.xvg | 8_1_1000.tpr | 8_1_1000_pullx.xvg | 8_1_1040.tpr | 8_1_1040_pullx.xvg | 8_1_1111.tpr | 8_1_1111_pullx.xvg | 8_1_1162.tpr | 8_1_1162_pullx.xvg | 8_1_1237.tpr | 8_1_1237_pullx.xvg | 8_1_1270.tpr | 8_1_1270_pullx.xvg | 8_1_1294.tpr | 8_1_1294_pullx.xvg | 8_1_133.tpr | 8_1_133_pullx.xvg | 8_1_221.tpr | 8_1_221_pullx.xvg | 8_1_293.tpr | 8_1_293_pullx.xvg | 8_1_311.tpr | 8_1_311_pullx.xvg | 8_1_32.tpr | 8_1_32_pullx.xvg | 8_1_382.tpr | 8_1_382_pullx.xvg | 8_1_493.tpr | 8_1_493_pullx.xvg | 8_1_526.tpr | 8_1_526_pullx.xvg | 8_1_6.tpr | 8_1_647.tpr | 8_1_647_pullx.xvg | 8_1_658.tpr | 8_1_658_pullx.xvg | 8_1_6_pullx.xvg | 8_1_793.tpr | 8_1_793_pullx.xvg | 8_1_822.tpr | 8_1_822_pullx.xvg | 8_1_855.tpr | 8_1_855_pullx.xvg | 8_1_929.tpr | 8_1_929_pullx.xvg | 8_1_95.tpr | 8_1_954.tpr | 8_1_954_pullx.xvg | 8_1_95_pullx.xvg | 8_1_961.tpr | 8_1_961_pullx.xvg | 8_1_970.tpr | 8_1_970_pullx.xvg | analyze_umbrella_blocks.sh | analyze_umbrella_final.sh | bsProfs_100-120ns.xvg | bsProfs_120ns-140ns.xvg | bsProfs_140-160ns.xvg | bsProfs_160-180ns.xvg | bsProfs_180-200ns.xvg | bsProfs_20-40ns.xvg | bsProfs_40-60ns.xvg | bsProfs_60-80ns.xvg | bsProfs_80-100ns.xvg | bsProfs_80-200ns.xvg | bsResult_100-120ns.xvg | bsResult_120-140ns.xvg | bsResult_140-160ns.xvg | bsResult_160-180ns.xvg | bsResult_180-200ns.xvg | bsResult_20-40ns.xvg | bsResult_40-60ns.xvg | bsResult_60-80ns.xvg | bsResult_80-100ns.xvg | bsResult_80-200ns.xvg | frames.dat | histo_100-120ns.xvg | histo_120-140ns.xvg | histo_140-160ns.xvg | histo_160-180ns.xvg | histo_180-200ns.xvg | histo_20-40ns.xvg | histo_40-60ns.xvg | histo_60-80ns.xvg | histo_80-100ns.xvg | histo_80-200ns.xvg | profile_100-120ns.xvg | profile_120-140ns.xvg | profile_140-160ns.xvg | profile_160-180ns.xvg | profile_180-200ns.xvg | profile_20-40ns.xvg | profile_40-60ns.xvg | profile_60-80ns.xvg | profile_80-100ns.xvg | profile_80-200ns.xvg | pullx_files.dat | tpr_files.dat | +---alphaI-unfold | +---eq | | | ATP.gro | | | ATP.itp | | | GLYM.gro | | | GLYM.itp | | | ionize.tpr | | | md.tpr | | | mdout.mdp | | | MG.gro | | | npt.gro | | | npt.mdp | | | npt.tpr | | | nvt.gro | | | nvt.mdp | | | nvt.tpr | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.gro | | | protein.itp | | | step6.0_minimization.mdp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_em.tpr | | | system_solv.gro | | | system_solv_ions.gro | | | topol_sys.top | | | | | +---1 | | | md.tpr | | | | | +---10 | | | md.tpr | | | | | +---2 | | | md.tpr | | | | | +---3 | | | md.tpr | | | | | +---4 | | | md.tpr | | | | | +---5 | | | md.tpr | | | | | +---6 | | | md.tpr | | | | | +---7 | | | md.tpr | | | | | +---8 | | | md.tpr | | | | | \---9 | | md.tpr | | | +---pull | | | ATP.itp | | | GLYM.itp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | protein.itp | | | pull_md.mdp | | | step6.0_minimization.mdp | | | topol.top | | | | | +---1 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---10 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---2 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---3 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---4 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---5 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---7 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---8 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | \---9 | | eq_md.gro | | npt.tpr | | nvt.tpr | | pull_em.tpr | | pull_md_0.05ms.tpr | | pull_md_0.1ms.tpr | | | \---umbrella | 10_05_1148.tpr | 10_05_1148_pullx.xvg | 10_05_1201.tpr | 10_05_1201_pullx.xvg | 10_05_1261.tpr | 10_05_1261_pullx.xvg | 10_05_1289.tpr | 10_05_1289_pullx.xvg | 10_05_1354.tpr | 10_05_1354_pullx.xvg | 10_05_1365.tpr | 10_05_1365_pullx.xvg | 10_05_1521.tpr | 10_05_1521_pullx.xvg | 10_05_1629.tpr | 10_05_1629_pullx.xvg | 10_05_1663.tpr | 10_05_1663_pullx.xvg | 10_05_1860.tpr | 10_05_1860_pullx.xvg | 10_05_1936.tpr | 10_05_1936_pullx.xvg | 10_05_196.tpr | 10_05_196_pullx.xvg | 10_05_334.tpr | 10_05_334_pullx.xvg | 10_05_34.tpr | 10_05_341.tpr | 10_05_341_pullx.xvg | 10_05_34_pullx.xvg | 10_05_382.tpr | 10_05_382_pullx.xvg | 10_05_653.tpr | 10_05_653_pullx.xvg | 10_05_753.tpr | 10_05_753_pullx.xvg | 10_05_803.tpr | 10_05_803_pullx.xvg | 10_05_968.tpr | 10_05_968_pullx.xvg | 10_05_997.tpr | 10_05_997_pullx.xvg | 10_1_100.tpr | 10_1_100_pullx.xvg | 10_1_103.tpr | 10_1_103_pullx.xvg | 10_1_124.tpr | 10_1_124_pullx.xvg | 10_1_13.tpr | 10_1_13_pullx.xvg | 10_1_198.tpr | 10_1_198_pullx.xvg | 10_1_309.tpr | 10_1_309_pullx.xvg | 10_1_348.tpr | 10_1_348_pullx.xvg | 10_1_376.tpr | 10_1_376_pullx.xvg | 10_1_419.tpr | 10_1_419_pullx.xvg | 10_1_501.tpr | 10_1_501_pullx.xvg | 10_1_552.tpr | 10_1_552_pullx.xvg | 10_1_576.tpr | 10_1_576_pullx.xvg | 10_1_686.tpr | 10_1_686_pullx.xvg | 10_1_693.tpr | 10_1_693_pullx.xvg | 10_1_70.tpr | 10_1_708.tpr | 10_1_708_pullx.xvg | 10_1_70_pullx.xvg | 10_1_778.tpr | 10_1_778_pullx.xvg | 10_1_785.tpr | 10_1_785_pullx.xvg | 10_1_792.tpr | 10_1_792_pullx.xvg | 10_1_839.tpr | 10_1_839_pullx.xvg | 10_1_878.tpr | 10_1_878_pullx.xvg | 10_1_88.tpr | 10_1_88_pullx.xvg | 10_1_897.tpr | 10_1_897_pullx.xvg | 10_1_931.tpr | 10_1_931_pullx.xvg | 10_1_977.tpr | 10_1_977_pullx.xvg | 1_05_105.tpr | 1_05_105_pullx.xvg | 1_05_1127.tpr | 1_05_1127_pullx.xvg | 1_05_1209.tpr | 1_05_1209_pullx.xvg | 1_05_1350.tpr | 1_05_1350_pullx.xvg | 1_05_1423.tpr | 1_05_1423_pullx.xvg | 1_05_1494.tpr | 1_05_1494_pullx.xvg | 1_05_1510.tpr | 1_05_1510_pullx.xvg | 1_05_1620.tpr | 1_05_1620_pullx.xvg | 1_05_1735.tpr | 1_05_1735_pullx.xvg | 1_05_1968.tpr | 1_05_1968_pullx.xvg | 1_05_2058.tpr | 1_05_2058_pullx.xvg | 1_05_2132.tpr | 1_05_2132_pullx.xvg | 1_05_2169.tpr | 1_05_2169_pullx.xvg | 1_05_241.tpr | 1_05_241_pullx.xvg | 1_05_299.tpr | 1_05_299_pullx.xvg | 1_05_32.tpr | 1_05_32_pullx.xvg | 1_05_370.tpr | 1_05_370_pullx.xvg | 1_05_410.tpr | 1_05_410_pullx.xvg | 1_05_524.tpr | 1_05_524_pullx.xvg | 1_05_664.tpr | 1_05_664_pullx.xvg | 1_05_769.tpr | 1_05_769_pullx.xvg | 1_05_871.tpr | 1_05_871_pullx.xvg | 1_05_998.tpr | 1_05_998_pullx.xvg | 1_1_0.tpr | 1_1_0_pullx.xvg | 1_1_1070.tpr | 1_1_1070_pullx.xvg | 1_1_109.tpr | 1_1_1093.tpr | 1_1_1093_pullx.xvg | 1_1_109_pullx.xvg | 1_1_266.tpr | 1_1_266_pullx.xvg | 1_1_456.tpr | 1_1_456_pullx.xvg | 1_1_512.tpr | 1_1_512_pullx.xvg | 1_1_58.tpr | 1_1_587.tpr | 1_1_587_pullx.xvg | 1_1_58_pullx.xvg | 1_1_628.tpr | 1_1_628_pullx.xvg | 1_1_661.tpr | 1_1_661_pullx.xvg | 1_1_692.tpr | 1_1_692_pullx.xvg | 1_1_7.tpr | 1_1_748.tpr | 1_1_748_pullx.xvg | 1_1_770.tpr | 1_1_770_pullx.xvg | 1_1_7_pullx.xvg | 1_1_823.tpr | 1_1_823_pullx.xvg | 1_1_849.tpr | 1_1_849_pullx.xvg | 1_1_908.tpr | 1_1_908_pullx.xvg | 1_1_996.tpr | 1_1_996_pullx.xvg | 2_05_109.tpr | 2_05_1093.tpr | 2_05_1093_pullx.xvg | 2_05_109_pullx.xvg | 2_05_1236.tpr | 2_05_1236_pullx.xvg | 2_05_1314.tpr | 2_05_1314_pullx.xvg | 2_05_133.tpr | 2_05_133_pullx.xvg | 2_05_1385.tpr | 2_05_1385_pullx.xvg | 2_05_1416.tpr | 2_05_1416_pullx.xvg | 2_05_1446.tpr | 2_05_1446_pullx.xvg | 2_05_1663.tpr | 2_05_1663_pullx.xvg | 2_05_168.tpr | 2_05_168_pullx.xvg | 2_05_1713.tpr | 2_05_1713_pullx.xvg | 2_05_1749.tpr | 2_05_1749_pullx.xvg | 2_05_1776.tpr | 2_05_1776_pullx.xvg | 2_05_186.tpr | 2_05_186_pullx.xvg | 2_05_1999.tpr | 2_05_1999_pullx.xvg | 2_05_2036.tpr | 2_05_2036_pullx.xvg | 2_05_2064.tpr | 2_05_2064_pullx.xvg | 2_05_224.tpr | 2_05_224_pullx.xvg | 2_05_235.tpr | 2_05_235_pullx.xvg | 2_05_25.tpr | 2_05_255.tpr | 2_05_255_pullx.xvg | 2_05_25_pullx.xvg | 2_05_268.tpr | 2_05_268_pullx.xvg | 2_05_337.tpr | 2_05_337_pullx.xvg | 2_05_799.tpr | 2_05_799_pullx.xvg | 2_05_961.tpr | 2_05_961_pullx.xvg | 2_05_982.tpr | 2_05_982_pullx.xvg | 2_1_1028.tpr | 2_1_1028_pullx.xvg | 2_1_107.tpr | 2_1_107_pullx.xvg | 2_1_187.tpr | 2_1_187_pullx.xvg | 2_1_216.tpr | 2_1_216_pullx.xvg | 2_1_253.tpr | 2_1_253_pullx.xvg | 2_1_269.tpr | 2_1_269_pullx.xvg | 2_1_361.tpr | 2_1_361_pullx.xvg | 2_1_517.tpr | 2_1_517_pullx.xvg | 2_1_612.tpr | 2_1_612_pullx.xvg | 2_1_65.tpr | 2_1_65_pullx.xvg | 2_1_670.tpr | 2_1_670_pullx.xvg | 2_1_673.tpr | 2_1_673_pullx.xvg | 2_1_732.tpr | 2_1_732_pullx.xvg | 2_1_762.tpr | 2_1_762_pullx.xvg | 2_1_815.tpr | 2_1_815_pullx.xvg | 2_1_949.tpr | 2_1_949_pullx.xvg | 2_1_957.tpr | 2_1_957_pullx.xvg | 2_1_96.tpr | 2_1_96_pullx.xvg | 2_1_970.tpr | 2_1_970_pullx.xvg | 4_05_1030.tpr | 4_05_1030_pullx.xvg | 4_05_104.tpr | 4_05_104_pullx.xvg | 4_05_1052.tpr | 4_05_1052_pullx.xvg | 4_05_1248.tpr | 4_05_1248_pullx.xvg | 4_05_1385.tpr | 4_05_1385_pullx.xvg | 4_05_1428.tpr | 4_05_1428_pullx.xvg | 4_05_145.tpr | 4_05_145_pullx.xvg | 4_05_1485.tpr | 4_05_1485_pullx.xvg | 4_05_1507.tpr | 4_05_1507_pullx.xvg | 4_05_154.tpr | 4_05_154_pullx.xvg | 4_05_1605.tpr | 4_05_1605_pullx.xvg | 4_05_161.tpr | 4_05_161_pullx.xvg | 4_05_1650.tpr | 4_05_1650_pullx.xvg | 4_05_1688.tpr | 4_05_1688_pullx.xvg | 4_05_1705.tpr | 4_05_1705_pullx.xvg | 4_05_1735.tpr | 4_05_1735_pullx.xvg | 4_05_1744.tpr | 4_05_1744_pullx.xvg | 4_05_179.tpr | 4_05_179_pullx.xvg | 4_05_197.tpr | 4_05_197_pullx.xvg | 4_05_238.tpr | 4_05_238_pullx.xvg | 4_05_402.tpr | 4_05_402_pullx.xvg | 4_05_588.tpr | 4_05_588_pullx.xvg | 4_05_76.tpr | 4_05_76_pullx.xvg | 4_05_885.tpr | 4_05_885_pullx.xvg | 4_05_987.tpr | 4_05_987_pullx.xvg | 4_1_152.tpr | 4_1_152_pullx.xvg | 4_1_178.tpr | 4_1_178_pullx.xvg | 4_1_200.tpr | 4_1_200_pullx.xvg | 4_1_255.tpr | 4_1_255_pullx.xvg | 4_1_258.tpr | 4_1_258_pullx.xvg | 4_1_471.tpr | 4_1_471_pullx.xvg | 4_1_496.tpr | 4_1_496_pullx.xvg | 4_1_523.tpr | 4_1_523_pullx.xvg | 4_1_538.tpr | 4_1_538_pullx.xvg | 4_1_566.tpr | 4_1_566_pullx.xvg | 4_1_579.tpr | 4_1_579_pullx.xvg | 4_1_602.tpr | 4_1_602_pullx.xvg | 4_1_610.tpr | 4_1_610_pullx.xvg | 4_1_665.tpr | 4_1_665_pullx.xvg | 4_1_676.tpr | 4_1_676_pullx.xvg | 4_1_719.tpr | 4_1_719_pullx.xvg | 4_1_737.tpr | 4_1_737_pullx.xvg | 4_1_74.tpr | 4_1_74_pullx.xvg | 4_1_757.tpr | 4_1_757_pullx.xvg | 4_1_792.tpr | 4_1_792_pullx.xvg | 4_1_811.tpr | 4_1_811_pullx.xvg | 5_05_102.tpr | 5_05_102_pullx.xvg | 5_05_1117.tpr | 5_05_1117_pullx.xvg | 5_05_1154.tpr | 5_05_1154_pullx.xvg | 5_05_1298.tpr | 5_05_1298_pullx.xvg | 5_05_1389.tpr | 5_05_1389_pullx.xvg | 5_05_147.tpr | 5_05_147_pullx.xvg | 5_05_1556.tpr | 5_05_1556_pullx.xvg | 5_05_1693.tpr | 5_05_1693_pullx.xvg | 5_05_1878.tpr | 5_05_1878_pullx.xvg | 5_05_1900.tpr | 5_05_1900_pullx.xvg | 5_05_2028.tpr | 5_05_2028_pullx.xvg | 5_05_2037.tpr | 5_05_2037_pullx.xvg | 5_05_318.tpr | 5_05_318_pullx.xvg | 5_05_471.tpr | 5_05_471_pullx.xvg | 5_05_480.tpr | 5_05_480_pullx.xvg | 5_05_652.tpr | 5_05_652_pullx.xvg | 5_05_732.tpr | 5_05_732_pullx.xvg | 5_05_830.tpr | 5_05_830_pullx.xvg | 5_05_887.tpr | 5_05_887_pullx.xvg | 5_05_979.tpr | 5_05_979_pullx.xvg | 5_1_1009.tpr | 5_1_1009_pullx.xvg | 5_1_1023.tpr | 5_1_1023_pullx.xvg | 5_1_13.tpr | 5_1_13_pullx.xvg | 5_1_144.tpr | 5_1_144_pullx.xvg | 5_1_245.tpr | 5_1_245_pullx.xvg | 5_1_283.tpr | 5_1_283_pullx.xvg | 5_1_41.tpr | 5_1_41_pullx.xvg | 5_1_516.tpr | 5_1_516_pullx.xvg | 5_1_53.tpr | 5_1_53_pullx.xvg | 5_1_583.tpr | 5_1_583_pullx.xvg | 5_1_592.tpr | 5_1_592_pullx.xvg | 5_1_611.tpr | 5_1_611_pullx.xvg | 5_1_62.tpr | 5_1_62_pullx.xvg | 5_1_631.tpr | 5_1_631_pullx.xvg | 5_1_644.tpr | 5_1_644_pullx.xvg | 5_1_673.tpr | 5_1_673_pullx.xvg | 5_1_683.tpr | 5_1_683_pullx.xvg | 5_1_70.tpr | 5_1_70_pullx.xvg | 5_1_722.tpr | 5_1_722_pullx.xvg | 5_1_782.tpr | 5_1_782_pullx.xvg | 5_1_807.tpr | 5_1_807_pullx.xvg | 5_1_966.tpr | 5_1_966_pullx.xvg | analyze_umbrella_blocks.sh | analyze_umbrella_final.sh | bsProfs_100-120ns.xvg | bsProfs_120-140ns.xvg | bsProfs_140-160ns.xvg | bsProfs_160-180ns.xvg | bsProfs_180-200ns.xvg | bsProfs_20-40ns.xvg | bsProfs_40-60ns.xvg | bsProfs_60-80ns.xvg | bsProfs_80-100ns.xvg | bsProfs_80-200ns.xvg | bsResult_100-120ns.xvg | bsResult_120-140ns.xvg | bsResult_140-160ns.xvg | bsResult_160-180ns.xvg | bsResult_180-200ns.xvg | bsResult_20-40ns.xvg | bsResult_40-60ns.xvg | bsResult_60-80ns.xvg | bsResult_80-100ns.xvg | bsResult_80-200ns.xvg | frames.dat | histo_100-120ns.xvg | histo_120-140ns.xvg | histo_140-160ns.xvg | histo_160-180ns.xvg | histo_180-200ns.xvg | histo_20-40ns.xvg | histo_40-60ns.xvg | histo_60-80ns.xvg | histo_80-100ns.xvg | histo_80-200ns.xvg | profile_100-120ns.xvg | profile_120-140ns.xvg | profile_140-160ns.xvg | profile_160-180ns.xvg | profile_180-200ns.xvg | profile_20-40ns.xvg | profile_40-60ns.xvg | profile_60-80ns.xvg | profile_80-100ns.xvg | profile_80-200ns.xvg | pullx_files.dat | tpr_files.dat | +---delta-alphaIb | +---eq | | | ATP.gro | | | ATP.itp | | | GLYM.gro | | | GLYM.itp | | | ionize.tpr | | | md.tpr | | | mdout.mdp | | | MG.gro | | | npt.gro | | | npt.mdp | | | npt.tpr | | | nvt.gro | | | nvt.mdp | | | nvt.tpr | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | production_md.mdp | | | protein.gro | | | protein.itp | | | step6.0_minimization.mdp | | | system.gro | | | system_box.gro | | | system_em.gro | | | system_em.tpr | | | system_solv.gro | | | system_solv_ions.gro | | | topol_sys.top | | | | | +---1 | | | md.tpr | | | | | +---10 | | | md.tpr | | | | | +---2 | | | md.tpr | | | | | +---3 | | | md.tpr | | | | | +---4 | | | md.tpr | | | | | +---5 | | | md.tpr | | | | | +---6 | | | md.tpr | | | | | +---7 | | | md.tpr | | | | | +---8 | | | md.tpr | | | | | \---9 | | md.tpr | | | +---pull | | | ATP.itp | | | GLYM.itp | | | mdout.mdp | | | npt.mdp | | | nvt.mdp | | | posre_ATP.itp | | | posre_GLYM.itp | | | posre_protein.itp | | | protein.itp | | | pull_md.mdp | | | step6.0_minimization.mdp | | | topol.top | | | | | +---1 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---2 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---3 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---4 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---5 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---6 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | +---7 | | | eq_md.gro | | | npt.tpr | | | nvt.tpr | | | pull_em.tpr | | | pull_md_0.05ms.tpr | | | pull_md_0.1ms.tpr | | | | | \---8 | | eq_md.gro | | npt.tpr | | nvt.tpr | | pull_em.tpr | | pull_md_0.05ms.tpr | | pull_md_0.1ms.tpr | | | \---umbrella | 1_05_100.tpr | 1_05_100_pullx.xvg | 1_05_115.tpr | 1_05_1156.tpr | 1_05_1156_pullx.xvg | 1_05_115_pullx.xvg | 1_05_1169.tpr | 1_05_1169_pullx.xvg | 1_05_1237.tpr | 1_05_1237_pullx.xvg | 1_05_1266.tpr | 1_05_1266_pullx.xvg | 1_05_1368.tpr | 1_05_1368_pullx.xvg | 1_05_200.tpr | 1_05_200_pullx.xvg | 1_05_269.tpr | 1_05_269_pullx.xvg | 1_05_36.tpr | 1_05_36_pullx.xvg | 1_05_392.tpr | 1_05_392_pullx.xvg | 1_05_416.tpr | 1_05_416_pullx.xvg | 1_05_51.tpr | 1_05_51_pullx.xvg | 1_05_609.tpr | 1_05_609_pullx.xvg | 1_05_7.tpr | 1_05_728.tpr | 1_05_728_pullx.xvg | 1_05_786.tpr | 1_05_786_pullx.xvg | 1_05_7_pullx.xvg | 1_05_854.tpr | 1_05_854_pullx.xvg | 1_05_878.tpr | 1_05_878_pullx.xvg | 1_05_905.tpr | 1_05_905_pullx.xvg | 1_05_928.tpr | 1_05_928_pullx.xvg | 1_05_957.tpr | 1_05_957_pullx.xvg | 1_1_121.tpr | 1_1_121_pullx.xvg | 1_1_15.tpr | 1_1_15_pullx.xvg | 1_1_177.tpr | 1_1_177_pullx.xvg | 1_1_183.tpr | 1_1_183_pullx.xvg | 1_1_200.tpr | 1_1_200_pullx.xvg | 1_1_21.tpr | 1_1_21_pullx.xvg | 1_1_239.tpr | 1_1_239_pullx.xvg | 1_1_308.tpr | 1_1_308_pullx.xvg | 1_1_359.tpr | 1_1_359_pullx.xvg | 1_1_406.tpr | 1_1_406_pullx.xvg | 1_1_427.tpr | 1_1_427_pullx.xvg | 1_1_44.tpr | 1_1_446.tpr | 1_1_446_pullx.xvg | 1_1_44_pullx.xvg | 1_1_46.tpr | 1_1_463.tpr | 1_1_463_pullx.xvg | 1_1_46_pullx.xvg | 1_1_479.tpr | 1_1_479_pullx.xvg | 1_1_503.tpr | 1_1_503_pullx.xvg | 1_1_509.tpr | 1_1_509_pullx.xvg | 1_1_53.tpr | 1_1_53_pullx.xvg | 1_1_590.tpr | 1_1_590_pullx.xvg | 1_1_632.tpr | 1_1_632_pullx.xvg | 1_1_677.tpr | 1_1_677_pullx.xvg | 1_1_7.tpr | 1_1_7_pullx.xvg | 2_05_1074.tpr | 2_05_1074_pullx.xvg | 2_05_108.tpr | 2_05_108_pullx.xvg | 2_05_1101.tpr | 2_05_1101_pullx.xvg | 2_05_1155.tpr | 2_05_1155_pullx.xvg | 2_05_1164.tpr | 2_05_1164_pullx.xvg | 2_05_1197.tpr | 2_05_1197_pullx.xvg | 2_05_1224.tpr | 2_05_1224_pullx.xvg | 2_05_1260.tpr | 2_05_1260_pullx.xvg | 2_05_1287.tpr | 2_05_1287_pullx.xvg | 2_05_1302.tpr | 2_05_1302_pullx.xvg | 2_05_1404.tpr | 2_05_1404_pullx.xvg | 2_05_1459.tpr | 2_05_1459_pullx.xvg | 2_05_1490.tpr | 2_05_1490_pullx.xvg | 2_05_153.tpr | 2_05_153_pullx.xvg | 2_05_1588.tpr | 2_05_1588_pullx.xvg | 2_05_2.tpr | 2_05_204.tpr | 2_05_204_pullx.xvg | 2_05_255.tpr | 2_05_255_pullx.xvg | 2_05_26.tpr | 2_05_26_pullx.xvg | 2_05_2_pullx.xvg | 2_05_306.tpr | 2_05_306_pullx.xvg | 2_05_339.tpr | 2_05_339_pullx.xvg | 2_05_387.tpr | 2_05_387_pullx.xvg | 2_05_464.tpr | 2_05_464_pullx.xvg | 2_05_646.tpr | 2_05_646_pullx.xvg | 2_05_720.tpr | 2_05_720_pullx.xvg | 2_05_80.tpr | 2_05_80_pullx.xvg | 2_05_830.tpr | 2_05_830_pullx.xvg | 2_05_902.tpr | 2_05_902_pullx.xvg | 2_1_1.tpr | 2_1_167.tpr | 2_1_167_pullx.xvg | 2_1_189.tpr | 2_1_189_pullx.xvg | 2_1_1_pullx.xvg | 2_1_219.tpr | 2_1_219_pullx.xvg | 2_1_23.tpr | 2_1_23_pullx.xvg | 2_1_263.tpr | 2_1_263_pullx.xvg | 2_1_298.tpr | 2_1_298_pullx.xvg | 2_1_305.tpr | 2_1_305_pullx.xvg | 2_1_310.tpr | 2_1_310_pullx.xvg | 2_1_368.tpr | 2_1_368_pullx.xvg | 2_1_427.tpr | 2_1_427_pullx.xvg | 2_1_478.tpr | 2_1_478_pullx.xvg | 2_1_51.tpr | 2_1_51_pullx.xvg | 2_1_522.tpr | 2_1_522_pullx.xvg | 2_1_576.tpr | 2_1_576_pullx.xvg | 2_1_623.tpr | 2_1_623_pullx.xvg | 2_1_631.tpr | 2_1_631_pullx.xvg | 2_1_648.tpr | 2_1_648_pullx.xvg | 2_1_658.tpr | 2_1_658_pullx.xvg | 2_1_666.tpr | 2_1_666_pullx.xvg | 2_1_672.tpr | 2_1_672_pullx.xvg | 2_1_696.tpr | 2_1_696_pullx.xvg | 2_1_707.tpr | 2_1_707_pullx.xvg | 2_1_763.tpr | 2_1_763_pullx.xvg | 2_1_78.tpr | 2_1_78_pullx.xvg | 2_1_832.tpr | 2_1_832_pullx.xvg | 2_1_842.tpr | 2_1_842_pullx.xvg | 2_1_85.tpr | 2_1_85_pullx.xvg | 4_05_112.tpr | 4_05_112_pullx.xvg | 4_05_1133.tpr | 4_05_1133_pullx.xvg | 4_05_1249.tpr | 4_05_1249_pullx.xvg | 4_05_1345.tpr | 4_05_1345_pullx.xvg | 4_05_1384.tpr | 4_05_1384_pullx.xvg | 4_05_1408.tpr | 4_05_1408_pullx.xvg | 4_05_1423.tpr | 4_05_1423_pullx.xvg | 4_05_1454.tpr | 4_05_1454_pullx.xvg | 4_05_1492.tpr | 4_05_1492_pullx.xvg | 4_05_155.tpr | 4_05_155_pullx.xvg | 4_05_1576.tpr | 4_05_1576_pullx.xvg | 4_05_1651.tpr | 4_05_1651_pullx.xvg | 4_05_1769.tpr | 4_05_1769_pullx.xvg | 4_05_193.tpr | 4_05_193_pullx.xvg | 4_05_206.tpr | 4_05_206_pullx.xvg | 4_05_258.tpr | 4_05_258_pullx.xvg | 4_05_315.tpr | 4_05_315_pullx.xvg | 4_05_339.tpr | 4_05_339_pullx.xvg | 4_05_350.tpr | 4_05_350_pullx.xvg | 4_05_464.tpr | 4_05_464_pullx.xvg | 4_05_60.tpr | 4_05_60_pullx.xvg | 4_05_639.tpr | 4_05_639_pullx.xvg | 4_05_708.tpr | 4_05_708_pullx.xvg | 4_05_824.tpr | 4_05_824_pullx.xvg | 4_05_845.tpr | 4_05_845_pullx.xvg | 4_05_990.tpr | 4_05_990_pullx.xvg | 4_1_13.tpr | 4_1_139.tpr | 4_1_139_pullx.xvg | 4_1_13_pullx.xvg | 4_1_151.tpr | 4_1_151_pullx.xvg | 4_1_183.tpr | 4_1_183_pullx.xvg | 4_1_185.tpr | 4_1_185_pullx.xvg | 4_1_231.tpr | 4_1_231_pullx.xvg | 4_1_253.tpr | 4_1_253_pullx.xvg | 4_1_296.tpr | 4_1_296_pullx.xvg | 4_1_34.tpr | 4_1_344.tpr | 4_1_344_pullx.xvg | 4_1_34_pullx.xvg | 4_1_403.tpr | 4_1_403_pullx.xvg | 4_1_409.tpr | 4_1_409_pullx.xvg | 4_1_42.tpr | 4_1_42_pullx.xvg | 4_1_481.tpr | 4_1_481_pullx.xvg | 4_1_490.tpr | 4_1_490_pullx.xvg | 4_1_495.tpr | 4_1_495_pullx.xvg | 4_1_528.tpr | 4_1_528_pullx.xvg | 4_1_544.tpr | 4_1_544_pullx.xvg | 4_1_64.tpr | 4_1_64_pullx.xvg | 4_1_656.tpr | 4_1_656_pullx.xvg | 4_1_67.tpr | 4_1_675.tpr | 4_1_675_pullx.xvg | 4_1_67_pullx.xvg | 4_1_684.tpr | 4_1_684_pullx.xvg | 4_1_7.tpr | 4_1_710.tpr | 4_1_710_pullx.xvg | 4_1_727.tpr | 4_1_727_pullx.xvg | 4_1_765.tpr | 4_1_765_pullx.xvg | 4_1_793.tpr | 4_1_793_pullx.xvg | 4_1_7_pullx.xvg | 4_1_830.tpr | 4_1_830_pullx.xvg | 4_1_872.tpr | 4_1_872_pullx.xvg | 5_05_1039.tpr | 5_05_1039_pullx.xvg | 5_05_1111.tpr | 5_05_1111_pullx.xvg | 5_05_1238.tpr | 5_05_1238_pullx.xvg | 5_05_1383.tpr | 5_05_1383_pullx.xvg | 5_05_14.tpr | 5_05_1468.tpr | 5_05_1468_pullx.xvg | 5_05_14_pullx.xvg | 5_05_1529.tpr | 5_05_1529_pullx.xvg | 5_05_163.tpr | 5_05_163_pullx.xvg | 5_05_1700.tpr | 5_05_1700_pullx.xvg | 5_05_1744.tpr | 5_05_1744_pullx.xvg | 5_05_1793.tpr | 5_05_1793_pullx.xvg | 5_05_180.tpr | 5_05_180_pullx.xvg | 5_05_1857.tpr | 5_05_1857_pullx.xvg | 5_05_1906.tpr | 5_05_1906_pullx.xvg | 5_05_2021.tpr | 5_05_2021_pullx.xvg | 5_05_2105.tpr | 5_05_2105_pullx.xvg | 5_05_2199.tpr | 5_05_2199_pullx.xvg | 5_05_2211.tpr | 5_05_2211_pullx.xvg | 5_05_2246.tpr | 5_05_2246_pullx.xvg | 5_05_2285.tpr | 5_05_2285_pullx.xvg | 5_05_2327.tpr | 5_05_2327_pullx.xvg | 5_05_240.tpr | 5_05_240_pullx.xvg | 5_05_2467.tpr | 5_05_2467_pullx.xvg | 5_05_2499.tpr | 5_05_2499_pullx.xvg | 5_05_33.tpr | 5_05_33_pullx.xvg | 5_05_349.tpr | 5_05_349_pullx.xvg | 5_05_391.tpr | 5_05_391_pullx.xvg | 5_05_404.tpr | 5_05_404_pullx.xvg | 5_05_421.tpr | 5_05_421_pullx.xvg | 5_05_513.tpr | 5_05_513_pullx.xvg | 5_05_556.tpr | 5_05_556_pullx.xvg | 5_05_72.tpr | 5_05_72_pullx.xvg | 5_05_763.tpr | 5_05_763_pullx.xvg | 5_05_824.tpr | 5_05_824_pullx.xvg | 5_05_976.tpr | 5_05_976_pullx.xvg | 5_1_0.tpr | 5_1_0_pullx.xvg | 5_1_1024.tpr | 5_1_1024_pullx.xvg | 5_1_1038.tpr | 5_1_1038_pullx.xvg | 5_1_1061.tpr | 5_1_1061_pullx.xvg | 5_1_1087.tpr | 5_1_1087_pullx.xvg | 5_1_1161.tpr | 5_1_1161_pullx.xvg | 5_1_117.tpr | 5_1_117_pullx.xvg | 5_1_122.tpr | 5_1_122_pullx.xvg | 5_1_143.tpr | 5_1_143_pullx.xvg | 5_1_173.tpr | 5_1_173_pullx.xvg | 5_1_19.tpr | 5_1_19_pullx.xvg | 5_1_207.tpr | 5_1_207_pullx.xvg | 5_1_241.tpr | 5_1_241_pullx.xvg | 5_1_305.tpr | 5_1_305_pullx.xvg | 5_1_355.tpr | 5_1_355_pullx.xvg | 5_1_431.tpr | 5_1_431_pullx.xvg | 5_1_456.tpr | 5_1_456_pullx.xvg | 5_1_50.tpr | 5_1_50_pullx.xvg | 5_1_511.tpr | 5_1_511_pullx.xvg | 5_1_55.tpr | 5_1_556.tpr | 5_1_556_pullx.xvg | 5_1_55_pullx.xvg | 5_1_615.tpr | 5_1_615_pullx.xvg | 5_1_659.tpr | 5_1_659_pullx.xvg | 5_1_70.tpr | 5_1_70_pullx.xvg | 5_1_751.tpr | 5_1_751_pullx.xvg | 5_1_803.tpr | 5_1_803_pullx.xvg | 5_1_827.tpr | 5_1_827_pullx.xvg | 5_1_877.tpr | 5_1_877_pullx.xvg | 5_1_881.tpr | 5_1_881_pullx.xvg | 5_1_938.tpr | 5_1_938_pullx.xvg | 5_1_952.tpr | 5_1_952_pullx.xvg | 5_1_959.tpr | 5_1_959_pullx.xvg | 5_1_990.tpr | 5_1_990_pullx.xvg | 6_05_1124.tpr | 6_05_1124_pullx.xvg | 6_05_1248.tpr | 6_05_1248_pullx.xvg | 6_05_1383.tpr | 6_05_1383_pullx.xvg | 6_05_1451.tpr | 6_05_1451_pullx.xvg | 6_05_1505.tpr | 6_05_1505_pullx.xvg | 6_05_1535.tpr | 6_05_1535_pullx.xvg | 6_05_1573.tpr | 6_05_1573_pullx.xvg | 6_05_1576.tpr | 6_05_1576_pullx.xvg | 6_05_1594.tpr | 6_05_1594_pullx.xvg | 6_05_1626.tpr | 6_05_1626_pullx.xvg | 6_05_1640.tpr | 6_05_1640_pullx.xvg | 6_05_1731.tpr | 6_05_1731_pullx.xvg | 6_05_1742.tpr | 6_05_1742_pullx.xvg | 6_05_1801.tpr | 6_05_1801_pullx.xvg | 6_05_1838.tpr | 6_05_1838_pullx.xvg | 6_05_2021.tpr | 6_05_2021_pullx.xvg | 6_05_204.tpr | 6_05_204_pullx.xvg | 6_05_2098.tpr | 6_05_2098_pullx.xvg | 6_05_2173.tpr | 6_05_2173_pullx.xvg | 6_05_221.tpr | 6_05_221_pullx.xvg | 6_05_278.tpr | 6_05_278_pullx.xvg | 6_05_305.tpr | 6_05_305_pullx.xvg | 6_05_32.tpr | 6_05_32_pullx.xvg | 6_05_4.tpr | 6_05_410.tpr | 6_05_410_pullx.xvg | 6_05_437.tpr | 6_05_437_pullx.xvg | 6_05_480.tpr | 6_05_480_pullx.xvg | 6_05_4_pullx.xvg | 6_05_543.tpr | 6_05_543_pullx.xvg | 6_05_58.tpr | 6_05_58_pullx.xvg | 6_05_668.tpr | 6_05_668_pullx.xvg | 6_05_738.tpr | 6_05_738_pullx.xvg | 6_05_873.tpr | 6_05_873_pullx.xvg | 6_05_978.tpr | 6_05_978_pullx.xvg | 6_05_99.tpr | 6_05_99_pullx.xvg | 6_1_1029.tpr | 6_1_1029_pullx.xvg | 6_1_136.tpr | 6_1_136_pullx.xvg | 6_1_140.tpr | 6_1_140_pullx.xvg | 6_1_148.tpr | 6_1_148_pullx.xvg | 6_1_171.tpr | 6_1_171_pullx.xvg | 6_1_22.tpr | 6_1_224.tpr | 6_1_224_pullx.xvg | 6_1_22_pullx.xvg | 6_1_233.tpr | 6_1_233_pullx.xvg | 6_1_29.tpr | 6_1_291.tpr | 6_1_291_pullx.xvg | 6_1_29_pullx.xvg | 6_1_322.tpr | 6_1_322_pullx.xvg | 6_1_404.tpr | 6_1_404_pullx.xvg | 6_1_447.tpr | 6_1_447_pullx.xvg | 6_1_482.tpr | 6_1_482_pullx.xvg | 6_1_543.tpr | 6_1_543_pullx.xvg | 6_1_62.tpr | 6_1_62_pullx.xvg | 6_1_647.tpr | 6_1_647_pullx.xvg | 6_1_654.tpr | 6_1_654_pullx.xvg | 6_1_711.tpr | 6_1_711_pullx.xvg | 6_1_73.tpr | 6_1_73_pullx.xvg | 6_1_762.tpr | 6_1_762_pullx.xvg | 6_1_8.tpr | 6_1_801.tpr | 6_1_801_pullx.xvg | 6_1_821.tpr | 6_1_821_pullx.xvg | 6_1_844.tpr | 6_1_844_pullx.xvg | 6_1_872.tpr | 6_1_872_pullx.xvg | 6_1_895.tpr | 6_1_895_pullx.xvg | 6_1_8_pullx.xvg | 6_1_919.tpr | 6_1_919_pullx.xvg | 6_1_962.tpr | 6_1_962_pullx.xvg | 6_1_983.tpr | 6_1_983_pullx.xvg | 8_05_106.tpr | 8_05_106_pullx.xvg | 8_05_1080.tpr | 8_05_1080_pullx.xvg | 8_05_1183.tpr | 8_05_1183_pullx.xvg | 8_05_16.tpr | 8_05_1656.tpr | 8_05_1656_pullx.xvg | 8_05_16_pullx.xvg | 8_05_1776.tpr | 8_05_1776_pullx.xvg | 8_05_192.tpr | 8_05_192_pullx.xvg | 8_05_1936.tpr | 8_05_1936_pullx.xvg | 8_05_1976.tpr | 8_05_1976_pullx.xvg | 8_05_2113.tpr | 8_05_2113_pullx.xvg | 8_05_2206.tpr | 8_05_2206_pullx.xvg | 8_05_2248.tpr | 8_05_2248_pullx.xvg | 8_05_2327.tpr | 8_05_2327_pullx.xvg | 8_05_2403.tpr | 8_05_2403_pullx.xvg | 8_05_2455.tpr | 8_05_2455_pullx.xvg | 8_05_2574.tpr | 8_05_2574_pullx.xvg | 8_05_2625.tpr | 8_05_2625_pullx.xvg | 8_05_2649.tpr | 8_05_2649_pullx.xvg | 8_05_266.tpr | 8_05_266_pullx.xvg | 8_05_296.tpr | 8_05_296_pullx.xvg | 8_05_30.tpr | 8_05_30_pullx.xvg | 8_05_351.tpr | 8_05_351_pullx.xvg | 8_05_374.tpr | 8_05_374_pullx.xvg | 8_05_403.tpr | 8_05_403_pullx.xvg | 8_05_519.tpr | 8_05_519_pullx.xvg | 8_05_543.tpr | 8_05_543_pullx.xvg | 8_05_657.tpr | 8_05_657_pullx.xvg | 8_05_76.tpr | 8_05_76_pullx.xvg | 8_05_814.tpr | 8_05_814_pullx.xvg | 8_1_1.tpr | 8_1_1019.tpr | 8_1_1019_pullx.xvg | 8_1_1080.tpr | 8_1_1080_pullx.xvg | 8_1_11.tpr | 8_1_1139.tpr | 8_1_1139_pullx.xvg | 8_1_1161.tpr | 8_1_1161_pullx.xvg | 8_1_1166.tpr | 8_1_1166_pullx.xvg | 8_1_1194.tpr | 8_1_1194_pullx.xvg | 8_1_11_pullx.xvg | 8_1_1201.tpr | 8_1_1201_pullx.xvg | 8_1_1228.tpr | 8_1_1228_pullx.xvg | 8_1_1241.tpr | 8_1_1241_pullx.xvg | 8_1_1276.tpr | 8_1_1276_pullx.xvg | 8_1_1307.tpr | 8_1_1307_pullx.xvg | 8_1_1437.tpr | 8_1_1437_pullx.xvg | 8_1_148.tpr | 8_1_148_pullx.xvg | 8_1_195.tpr | 8_1_195_pullx.xvg | 8_1_1_pullx.xvg | 8_1_21.tpr | 8_1_21_pullx.xvg | 8_1_231.tpr | 8_1_231_pullx.xvg | 8_1_271.tpr | 8_1_271_pullx.xvg | 8_1_299.tpr | 8_1_299_pullx.xvg | 8_1_315.tpr | 8_1_315_pullx.xvg | 8_1_353.tpr | 8_1_353_pullx.xvg | 8_1_387.tpr | 8_1_387_pullx.xvg | 8_1_498.tpr | 8_1_498_pullx.xvg | 8_1_550.tpr | 8_1_550_pullx.xvg | 8_1_634.tpr | 8_1_634_pullx.xvg | 8_1_649.tpr | 8_1_649_pullx.xvg | 8_1_773.tpr | 8_1_773_pullx.xvg | 8_1_80.tpr | 8_1_80_pullx.xvg | 8_1_818.tpr | 8_1_818_pullx.xvg | analyze_umbrella_blocks.sh | analyze_umbrella_final.sh | bsProfs_100-120ns.xvg | bsProfs_120-140ns.xvg | bsProfs_140-160ns.xvg | bsProfs_160-180ns.xvg | bsProfs_180-200ns.xvg | bsProfs_20-40ns.xvg | bsProfs_40-60ns.xvg | bsProfs_60-80ns.xvg | bsProfs_80-100ns.xvg | bsProfs_80-200ns.xvg | bsResult_100-120ns.xvg | bsResult_120-140ns.xvg | bsResult_140-160ns.xvg | bsResult_160-180ns.xvg | bsResult_180-200ns.xvg | bsResult_20-40ns.xvg | bsResult_40-60ns.xvg | bsResult_60-80ns.xvg | bsResult_80-100ns.xvg | bsResult_80-200ns.xvg | frames.dat | histo_100-120ns.xvg | histo_120-140ns.xvg | histo_140-160ns.xvg | histo_160-180ns.xvg | histo_180-200ns.xvg | histo_20-40ns.xvg | histo_40-60ns.xvg | histo_60-80ns.xvg | histo_80-100ns.xvg | histo_80-200ns.xvg | profile_100-120ns.xvg | profile_120-140ns.xvg | profile_140-160ns.xvg | profile_160-180ns.xvg | profile_180-200ns.xvg | profile_20-40ns.xvg | profile_40-60ns.xvg | profile_60-80ns.xvg | profile_80-100ns.xvg | profile_80-200ns.xvg | pullx_files.dat | tpr_files.dat | \---membrane +---eq | | GLYM.itp | | md_eq.mdp | | npt1.mdp | | npt1.tpr | | npt2.mdp | | npt2.tpr | | nvt.mdp | | nvt.tpr | | POPC.itp | | posre_GLYM.itp | | posre_POPC.itp | | system_em.gro | | topol.top | | | +---1 | | md_eq.tpr | | | +---2 | | md_eq.tpr | | | \---3 | md_eq.tpr | +---pull | | GLYM.itp | | ndx_groups_pull | | npt.mdp | | nvt.mdp | | POPC.itp | | posre_GLYM.itp | | posre_POPC.itp | | pull_md.mdp | | pull_setup.sh | | step6.0_minimization.mdp | | topol.top | | | +---1 | | last_frame_mol.gro | | npt.tpr | | nvt.tpr | | pull_em.tpr | | pull_md_0.05ms.tpr | | pull_md_0.1ms.tpr | | | +---2 | | last_frame_mol.gro | | npt.tpr | | nvt.tpr | | pull_em.tpr | | pull_md_0.05ms.tpr | | pull_md_0.1ms.tpr | | | \---3 | last_frame_mol.gro | npt.tpr | nvt.tpr | pull_em.tpr | pull_md_0.05ms.tpr | pull_md_0.1ms.tpr | \---umbrella 1_05_1009.tpr 1_05_1009_pullx.xvg 1_05_1054.tpr 1_05_1054_pullx.xvg 1_05_115.tpr 1_05_115_pullx.xvg 1_05_1187.tpr 1_05_1187_pullx.xvg 1_05_1234.tpr 1_05_1234_pullx.xvg 1_05_189.tpr 1_05_189_pullx.xvg 1_05_196.tpr 1_05_196_pullx.xvg 1_05_223.tpr 1_05_223_pullx.xvg 1_05_25.tpr 1_05_25_pullx.xvg 1_05_304.tpr 1_05_304_pullx.xvg 1_05_43.tpr 1_05_43_pullx.xvg 1_05_565.tpr 1_05_565_pullx.xvg 1_05_59.tpr 1_05_59_pullx.xvg 1_05_675.tpr 1_05_675_pullx.xvg 1_05_714.tpr 1_05_714_pullx.xvg 1_05_73.tpr 1_05_73_pullx.xvg 1_05_77.tpr 1_05_77_pullx.xvg 1_05_822.tpr 1_05_822_pullx.xvg 1_05_83.tpr 1_05_83_pullx.xvg 1_05_906.tpr 1_05_906_pullx.xvg 1_05_96.tpr 1_05_96_pullx.xvg 1_1_0.tpr 1_1_0_pullx.xvg 1_1_152.tpr 1_1_152_pullx.xvg 1_1_159.tpr 1_1_159_pullx.xvg 1_1_213.tpr 1_1_213_pullx.xvg 1_1_220.tpr 1_1_220_pullx.xvg 1_1_301.tpr 1_1_301_pullx.xvg 1_1_374.tpr 1_1_374_pullx.xvg 1_1_397.tpr 1_1_397_pullx.xvg 1_1_408.tpr 1_1_408_pullx.xvg 1_1_433.tpr 1_1_433_pullx.xvg 1_1_552.tpr 1_1_552_pullx.xvg 1_1_563.tpr 1_1_563_pullx.xvg 1_1_611.tpr 1_1_611_pullx.xvg 1_1_698.tpr 1_1_698_pullx.xvg 1_1_748.tpr 1_1_748_pullx.xvg 1_1_78.tpr 1_1_783.tpr 1_1_783_pullx.xvg 1_1_78_pullx.xvg 1_1_865.tpr 1_1_865_pullx.xvg 1_1_88.tpr 1_1_88_pullx.xvg 1_1_924.tpr 1_1_924_pullx.xvg 1_1_991.tpr 1_1_991_pullx.xvg 2_05_1051.tpr 2_05_1051_pullx.xvg 2_05_1132.tpr 2_05_1132_pullx.xvg 2_05_12.tpr 2_05_1273.tpr 2_05_1273_pullx.xvg 2_05_12_pullx.xvg 2_05_134.tpr 2_05_134_pullx.xvg 2_05_139.tpr 2_05_1391.tpr 2_05_1391_pullx.xvg 2_05_139_pullx.xvg 2_05_143.tpr 2_05_143_pullx.xvg 2_05_1526.tpr 2_05_1526_pullx.xvg 2_05_1649.tpr 2_05_1649_pullx.xvg 2_05_170.tpr 2_05_170_pullx.xvg 2_05_180.tpr 2_05_180_pullx.xvg 2_05_184.tpr 2_05_184_pullx.xvg 2_05_190.tpr 2_05_190_pullx.xvg 2_05_259.tpr 2_05_259_pullx.xvg 2_05_3.tpr 2_05_30.tpr 2_05_30_pullx.xvg 2_05_38.tpr 2_05_38_pullx.xvg 2_05_392.tpr 2_05_392_pullx.xvg 2_05_3_pullx.xvg 2_05_433.tpr 2_05_433_pullx.xvg 2_05_472.tpr 2_05_472_pullx.xvg 2_05_513.tpr 2_05_513_pullx.xvg 2_05_58.tpr 2_05_58_pullx.xvg 2_05_650.tpr 2_05_650_pullx.xvg 2_05_66.tpr 2_05_66_pullx.xvg 2_05_842.tpr 2_05_842_pullx.xvg 2_1_172.tpr 2_1_172_pullx.xvg 2_1_185.tpr 2_1_185_pullx.xvg 2_1_196.tpr 2_1_196_pullx.xvg 2_1_2.tpr 2_1_202.tpr 2_1_202_pullx.xvg 2_1_217.tpr 2_1_217_pullx.xvg 2_1_231.tpr 2_1_231_pullx.xvg 2_1_238.tpr 2_1_238_pullx.xvg 2_1_256.tpr 2_1_256_pullx.xvg 2_1_265.tpr 2_1_265_pullx.xvg 2_1_266.tpr 2_1_266_pullx.xvg 2_1_267.tpr 2_1_267_pullx.xvg 2_1_2_pullx.xvg 2_1_41.tpr 2_1_41_pullx.xvg 2_1_428.tpr 2_1_428_pullx.xvg 2_1_454.tpr 2_1_454_pullx.xvg 2_1_476.tpr 2_1_476_pullx.xvg 2_1_51.tpr 2_1_51_pullx.xvg 2_1_529.tpr 2_1_529_pullx.xvg 2_1_54.tpr 2_1_54_pullx.xvg 2_1_614.tpr 2_1_614_pullx.xvg 2_1_642.tpr 2_1_642_pullx.xvg 2_1_65.tpr 2_1_65_pullx.xvg 2_1_720.tpr 2_1_720_pullx.xvg 2_1_772.tpr 2_1_772_pullx.xvg 2_1_797.tpr 2_1_797_pullx.xvg 2_1_859.tpr 2_1_859_pullx.xvg 2_1_91.tpr 2_1_91_pullx.xvg 2_1_935.tpr 2_1_935_pullx.xvg 3_05_1009.tpr 3_05_1009_pullx.xvg 3_05_112.tpr 3_05_1128.tpr 3_05_1128_pullx.xvg 3_05_112_pullx.xvg 3_05_1194.tpr 3_05_1194_pullx.xvg 3_05_1196.tpr 3_05_1196_pullx.xvg 3_05_1374.tpr 3_05_1374_pullx.xvg 3_05_1448.tpr 3_05_1448_pullx.xvg 3_05_146.tpr 3_05_146_pullx.xvg 3_05_1512.tpr 3_05_1512_pullx.xvg 3_05_1603.tpr 3_05_1603_pullx.xvg 3_05_163.tpr 3_05_163_pullx.xvg 3_05_1756.tpr 3_05_1756_pullx.xvg 3_05_1788.tpr 3_05_1788_pullx.xvg 3_05_180.tpr 3_05_180_pullx.xvg 3_05_266.tpr 3_05_266_pullx.xvg 3_05_293.tpr 3_05_293_pullx.xvg 3_05_317.tpr 3_05_317_pullx.xvg 3_05_36.tpr 3_05_36_pullx.xvg 3_05_444.tpr 3_05_444_pullx.xvg 3_05_494.tpr 3_05_494_pullx.xvg 3_05_592.tpr 3_05_592_pullx.xvg 3_05_63.tpr 3_05_63_pullx.xvg 3_05_707.tpr 3_05_707_pullx.xvg 3_05_864.tpr 3_05_864_pullx.xvg 3_05_96.tpr 3_05_96_pullx.xvg 3_1_0.tpr 3_1_0_pullx.xvg 3_1_132.tpr 3_1_132_pullx.xvg 3_1_159.tpr 3_1_159_pullx.xvg 3_1_160.tpr 3_1_160_pullx.xvg 3_1_169.tpr 3_1_169_pullx.xvg 3_1_176.tpr 3_1_176_pullx.xvg 3_1_289.tpr 3_1_289_pullx.xvg 3_1_312.tpr 3_1_312_pullx.xvg 3_1_32.tpr 3_1_32_pullx.xvg 3_1_375.tpr 3_1_375_pullx.xvg 3_1_4.tpr 3_1_41.tpr 3_1_41_pullx.xvg 3_1_430.tpr 3_1_430_pullx.xvg 3_1_454.tpr 3_1_454_pullx.xvg 3_1_4_pullx.xvg 3_1_527.tpr 3_1_527_pullx.xvg 3_1_561.tpr 3_1_561_pullx.xvg 3_1_591.tpr 3_1_591_pullx.xvg 3_1_622.tpr 3_1_622_pullx.xvg 3_1_696.tpr 3_1_696_pullx.xvg 3_1_790.tpr 3_1_790_pullx.xvg 3_1_806.tpr 3_1_806_pullx.xvg 3_1_857.tpr 3_1_857_pullx.xvg 3_1_86.tpr 3_1_86_pullx.xvg 3_1_872.tpr 3_1_872_pullx.xvg 3_1_914.tpr 3_1_914_pullx.xvg 3_1_95.tpr 3_1_95_pullx.xvg analyze_umbrella_blocks.sh analyze_umbrella_final.sh bsProfs_100-120ns.xvg bsProfs_120-140ns.xvg bsProfs_140-160ns.xvg bsProfs_160-180ns.xvg bsProfs_180-200ns.xvg bsProfs_20-40ns.xvg bsProfs_40-60ns.xvg bsProfs_60-80ns.xvg bsProfs_80-100ns.xvg bsProfs_80-200ns.xvg bsResult_100-120ns.xvg bsResult_120-140ns.xvg bsResult_140-160ns.xvg bsResult_160-180ns.xvg bsResult_180-200ns.xvg bsResult_20-40ns.xvg bsResult_40-60ns.xvg bsResult_60-80ns.xvg bsResult_80-100ns.xvg bsResult_80-200ns.xvg frames.dat histo_100-120ns.xvg histo_120-140ns.xvg histo_140-160ns.xvg histo_160-180ns.xvg histo_180-200ns.xvg histo_20-40ns.xvg histo_40-60ns.xvg histo_60-80ns.xvg histo_80-100ns.xvg histo_80-200ns.xvg profile_100-120ns.xvg profile_120-140ns.xvg profile_140-160ns.xvg profile_160-180ns.xvg profile_180-200ns.xvg profile_20-40ns.xvg profile_40-60ns.xvg profile_60-80ns.xvg profile_80-100ns.xvg profile_80-200ns.xvg pullx_files.dat tpr_files.dat ```