cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3335503
title: Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field

description: Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field parameters, SPC/E water model and ECC-ions. file names report molar fraction of cations (i.e. not bulk concentrations) simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files) simulation length 300 ns temperature 313 K (otherwise noted) Gromacs simulation setting is in the file npt_lipid_bilayer.mdp
DOI: 10.5281/zenodo.3434396
title: CHARMM36, NB-Fix approaches, without NBFIX, POPC membrane, Ca, Na ions,

description: Different versions of NB-Fix from CHARMM-Gui and simulations without NB-Fix (called original charmm) 200 POPC lipids, TIP3P - charrmm water model,
DOI: 10.5281/zenodo.7586915
title: Pure POPC Membrane with 350mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 41 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7596011
title: Pure POPC Membrane with 650mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 77 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7600326
title: Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7600827
title: Pure POPC Membrane with 350mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 41 CaCl2, and 6400 SWM4 water molecules. wrapped.dcd has a frame saving frequency of 100 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7604040
title: Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 76 CaCl2, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. The initial structures have been obtained from CHARMM-GUI. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7604627
title: Pure POPE membrane simulations with the CHARMM-Drude force field (OpenMM 7.5.0)

description: MD simulation data of a pure POPE membrane with the CHARMM-Drude force field generated with the OpenMM 7.5.0 simulation engine. All the input parameters are available in the *inp file. The initial structures have been obtained from CHARMM-GUI. Total simulation duration is 300 ns (100 ns x 3, continuing from the last frame, combined with the mdconvert). First 50 ns is discarded as equilibration. This data set contains 300 ns data with 3000 frames (saving frequency is 100 ps). In total, 72 POPC lipids in each leaflet (144 in total), 5040 SWM4-NPD water molecules. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 100 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 3 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7604681
title: MD Simulation data for a pure DOPC bilayer without salt with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids and 2880 water molecules. The trajectory is 201,61 ns long (20161 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7604711
title: MD Simulation data for a pure DOPC bilayer (450 mM NaCl) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 450 mM NaCl with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 17 NaCl ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7604810
title: MD Simulation data for a pure DOPC bilayer (1000 mM CaCl2) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 1000 mM CaCl2 with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 36 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7604842
title: MD Simulation data for a pure DOPC bilayer (450 mM CaCl2) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 450 mM CaCl2 with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 16 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7605016
title: Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 52 CaCl2, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Frames are saved in every 10 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were centered with VMD command "pbc wrap -center origin -centersel lipid -compound residue -all", concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7607436
title: Pure POPC membrane simulations with the CHARMM-Drude force field (OpenMM 7.5.0)

description: MD simulation data of a pure POPC membrane with the CHARMM-Drude force field. All the input parameters are available in the *inp file. Total simulation duration is 500 ns. First 100 ns is discarded as equilibration. This data set contains 400 ns data with 40000 frames (saving frequency is 10 ps). In total, 64 POPC lipids in each leaflet, 6400 SWM4-NPD water molecules. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. The correction to the timestamp was done via MDAnalysis.</strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong>
DOI: 10.5281/zenodo.7625844
title: MD Simulation data for a pure DOPC bilayer (1000 mM NaCl) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 1000 mM NaCl with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 35 NaCl ions, and 2880 water molecules. The trajectory is 201,61 ns long (20161 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7658975
title: Pure POPC membrane simulations with 1000 mM CaCl2 with the CHARMM-Drude force field (OpenMM)

description: 400 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 114 CaCl2, and 6400 SWM4 water molecules. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. Total simulation time is 500 ns, included data is 397.5 ns. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps and there are 39750 frames.</strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 4 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong> <strong>Centering of the trajectories has been done via below MDAnalysis script</strong> <strong> ...: u = mda.Universe('../step3_charmm2omm.psf', 'step5.dcd')<br> ...: prot = u.select_atoms("resname POPC")<br> ...: ag = u.atoms<br> ...: workflow = (transformations.unwrap(ag),<br> ...: transformations.center_in_box(prot, center='mass'),<br> ...: transformations.wrap(ag, compound='fragments'))<br> ...: u.trajectory.add_transformations(*workflow)</strong>
DOI: 10.5281/zenodo.7871949
title: OpenMM simulations of POPC using the CHARMM Drude2023 force field

description: PSF, single CRD file, and DCD format trajectories for the final 200 ns of triplicate POPC simulations, from the publication <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda* https://doi.org/10.1021/acs.jctc.3c00203 DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file; each file has frames spaced at 10 ps over a 50 ns interval.
description: The data files contain additional atom types for the Drude particles and oxygen lone pairs
DOI: 10.5281/zenodo.7872447
title: OpenMM simulations of POPE using the CHARMM Drude2023 force field

description: <br> The dataset contains a PSF, a formatted coordinate file (CRD), and DCD files with the final 200 ns from<br> each of 3 replicate simulations from the paper <br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203 <br> DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file; each file has frames spaced at 10 ps over a 50 ns interval.
description: The data files contain additional atom types for the Drude particles and oxygen lone pairs