DOI: 10.15129/d6f658eb-9322-4006-be8b-ac33a562862b
title: Data for: Synthetic Flagella Spin and Contract at the Expense of Chemical Fuel

description: Due to limitations on file size for this dataset, trajectory files are provided in the GROMACS 
(.xtc) format, with the omission of water molecules (hence _dry.*) and for the last 5 ns of the 25 ns simulations. It is this portion of the simulation which was measured for the results described in the article. 

Contents:

 &gt; ForceField.zip: contains the NAMD compatible martini-par and martini-top files alongside the NAMD
 CpHMD executable *tcl file. 

 &gt; Fmoc: contains the *top files for FmocAVD/FmocAAD/FmocVVD as well as for the Fmoc group.

 &gt; Reference: contains all files and results for alchemical fitting of delta-G values for the
 anhydride group and its state switching between doubly and singly charged termini.

 &gt; Bilayer_grid_{2-4}: contain triplicate results for simulation of FmocAVD at various fuel levels 
 (e.g., from pH 1 - 4) which capture 100 - 0 % anhydride functionalisation. It is important to note
 that the 'pH' set in a given dir is not reflective of the 'number' of the directory (e.g., FL5 = 3.40
 and FL6 = 3.80). This convention was maintained for consistency with earlier results. 

 &gt; pulled_{dirname}_{property}.csv -- contain measurements reported in the article. 
 
 ~~~~ subdir ~~~~
 &gt; cphmd_dry.{xtc/gro} -- the dry, 5 ns trajectory of the bilayer at the end of the 25 ns eq. 
 &gt; cphmd_out2.{psf/pdb} -- use these to visualise the structure at the end of the simulation. 
 &gt; CPHLOG file details the charge state of each termini with the following meaning:
 
 0 0 = doubly deprotonated
 0 1 = singly deprotonated
 1 0 = singly deprotonated
 1 1 = anhydride functionality 

 &gt; CPHMD2.inp -- this is the run parameter file 
 &gt; CPHMD2.out -- this is the run output file. 
 &gt; The executable is as follows, note the specially compiled version of NAMD_2.14 (included in this dataset)

 /users/fjb15167/Constant_pH/NAMD_2.14_Source/Linux-x86_64-g++/namd2 +p$SLURM_NTASKS CPHMD2.inp &gt; CPHMD2.out

 &gt; Bilayer_grid_structure_equilibrate: this file contains the equilibration of the starting structure for the simulation
 of Bilayer_grid_{2-4} using straight MD (no CPHMD) and it is the coords/vels/xsc data pertained in these which are used
 as inputs for the CPHMD simulations. 

 &gt; Fmoc{AVD/AAD/VVD}_grid_{n}: these directories contain the run files for the different tripeptide 
 types at fuel levels FL1, FL3, FL7, FL8 and FL9. 
 
 &gt; Fmoc{AVD/AAD/VVD}__structure_equilibrate: building and equilibration of system starting structures using 100 %
 anhydride and no CPHMD method applied (e.g., straight MD equilibration). 
 
 &gt; Scripts: this dir contains all relevant python scripts for the analysis of these systems
 
 
 states_neighbours_master_3.0.py parses to identify the population of the anhydride/non-anhydride (execute first).
 
 analysis_master_3.0.py performs analysis of RDFs, dihedral stacking, SASA, length etc. 

 fresh_analysis.py is then used to nicely organise all output data into menagable formats for collaborators. These
 are saved as pulled_{dirname}_{property}.csv. 

 &gt; NAMD_2.14_Source: this contains the specially compiled version of NAMD which is required to run CPHMD simulations and this
 must be made accessible in the *inp file for this mode of simulation.