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51 results for “openMM”
Pure POPC Membrane Simulation Using Charmm-Drude Force Field with OpenMM
<p>400 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 72 POPC lipids and 2809 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>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.</p> <p>This dataset does not contain the water molecules.</p> <p><strong>Please note that</strong> the trajectories might need to be realigned.</p>
Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>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.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>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.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p>
Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 51 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>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.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p>
Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>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.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>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.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p>The initial structures have been obtained from CHARMM-GUI.</p> <p> </p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p>
Pure POPE membrane simulations with the CHARMM-Drude force field (OpenMM 7.5.0)
<p>MD simulation data of a pure POPE membrane with the CHARMM-Drude force field generated with the OpenMM 7.5.0 simulation engine.</p> <p>All the input parameters are available in the *inp file. The initial structures have been obtained from CHARMM-GUI.</p> <p>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).</p> <p>In total, 72 POPC lipids in each leaflet (144 in total), 5040 SWM4-NPD water molecules.</p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p> <p> </p> <p> </p>
Pure POPC Membrane with 350mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>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.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p>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.</p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p>
Pure POPC membrane simulations with 1000 mM CaCl2 with the CHARMM-Drude force field (OpenMM)
<p>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.</p> <p>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.</p> <p> </p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p> <p><strong>Centering of the trajectories has been done via below MDAnalysis script</strong></p> <p><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></p> <p> </p>
POPC lipid membrane, 303K, Charmm36 force field, simulation files and 200 ns trajectory for openMM simulation engine v7
<p>POPC lipid membrane, 303K, Charmm36 force field, simulation files and 200 ns trajectory for for openMM simulation engine v7</p> <p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 5120 tip3p waters, 200ns trajectory (preceded with equilibration).</p> <p>Note that the provided trajectories are in Gromacs XTC format, whereas NAMD DCD format was generated by openMM. This required trajectory conversion using Gromacs package (v5.1.2) with binary topology file from https://doi.org/10.5281/zenodo.153944 </p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field, simulation files and 100 ns trajectory for openMM simulation engine v7
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 84 POPC and 36 Cholesterol molecules, 4800 tip3p waters, 100ns trajectory (preceded with equilibration).</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
POPC/Cholesterol (50:50) lipid membrane, 303K, Charmm36 force field from charmm-gui, simulation files and 100 ns trajectory for openMM simulation engine v7
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 80 POPC and 80 Cholesterol molecules, 7200 tip3p waters, 100ns trajectory (preceded with equilibration)</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field through the use of Gromacs input files, simulation files and 100 ns trajectory for openMM simulation engine v7
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Specifically, Gromacs file format provided by [1] was specifically used for this simulation.</p> <p>Conditions: T=303, 84 POPC and 36 Cholesterol molecules, 4800 tip3p waters, 100ns trajectory (preceded with equilibration).</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 1)
<p>Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the first independent simulation runs out of 3.</p> <p>Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps.</p> <p>The system contains ~ 150 mM NaCl.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 2)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the second out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the third out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
Amyloid-beta 16-22 peptide dimer simulation (without salt) with the CHARMM-Drude force field and OpenMM (Run 1)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 0 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the first out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p>
DPPC lipid bilayer simulation with CHARMM36-LJPME force field using OpenMM
<p>DPPC lipid bilayer simulation (300 ns) with CHARMM36-LJPME force field using OpenMM at 323K.</p> <p>Used in <a href="http://doi.org/10.1021/acs.jctc.1c00951">https://doi.org/10.1021/acs.jctc.1c00951</a></p> <p>The force field parameters were downloaded from <a href="https://terpconnect.umd.edu/%7Ejbklauda/ff.html">https://terpconnect.umd.edu/%7Ejbklauda/ff.html</a>.</p> <p><a href="https://zenodo.org/api/files/1e89f677-91a8-472d-aebb-144fddd58d23/trajCORRECT1-2.dcd?versionId=5317fd88-6b98-4905-b171-53c1cd199cfe">trajCORRECT1-2.dcd </a>has incorrect timestamps. traj1-2.xtc has correct timestamps.<br> </p>
Pure POPE membrane simulations with the CHARMM-Drude force field at 310K (OpenMM)
<p>MD simulation data of a pure POPE membrane with the CHARMM-Drude force field generated with the OpenMM simulation engine at 310K.</p> <p>Parameters from CHARMM-GUI.</p>
MD Simulation data for a pure DOPC bilayer without salt with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids and 2880 water molecules. The trajectory is 201,61 ns long (20161 frames with 10 ps saving frequency).</p> <p><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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><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></p> <p> </p>
MD Simulation data for a pure POPE bilayer with AMOEBA force field + OpenMM
<p>MD simulation data for the POPE bilayer with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 POPE lipids and 2880 water molecules. The trajectory is 305,94 ns long (30594 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the openmm_combined.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></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p> </p>
OpenMM simulations of DLPC using the CHARMM Drude2023 force field
<p>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</p> <p><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</p> <p><br> DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file<br> Each file has 50 ns of data, with coordinate sets spaced at 10 ps between frames.</p>
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