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Dataset results
306 results for “POPC”
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>
MacRog pure POPC MD simulation (300 K - 500ns - 1 bar)
<p>MacRog POPC pure bilayer simulation. Starting structure from CHARMM-GUI: the initial PDB file was modified to match MacRog nomenclature and atom order. Temperature was set to 300 K and pressure to 1 bar with 128 POPC lipids fully hydrated: 40 water molecules per lipid. The trajectory contains the whole simulation from 0 to 500 ns skipped every 100 ps and centered on the P atoms. No ions were added as there is no charge in the system. This bilayer was used to calculate the order parameter and the area per lipid for the NMRLipids project (on the time window 200-500 ns).</p> <p>The popc.itp file was obtained from the paper doi : 10.1016/j.dib.2016.03.067. Several corrections have been made to the original file (for more information, go check <a href="https://www.dsimb.inserm.fr/~fuchs/project_Samuli/POPC_POPE/report_results_comparison.pdf">https://www.dsimb.inserm.fr/~fuchs/project_Samuli/POPC_POPE/report_results_comparison.pdf</a>). We provide here the corrected itp file.</p>
CHARMM36 simulations of pure POPC bilayer and a bilayer containing 50% of cholesterol, T=303K
<p>Simulation of POPC and 50%POPC+50%cholesterol bilayer in full hydration (40 water/lipid) at T=303K in NPT ensemble. Simulations where done on GPU Gromacs 2020.1. The initial configurations and force field (CHARMM36) were dowloaded from CHARMM-GUI. Simulation uses Parrinello-Rahman barostat and Nose-Hoover thermostat.</p>
Pure POPC membrane simulations using Amber Lipid 14 Force Field
<p>Pure POPC membrane simulations using the Amber Lipid 14 force field.</p> <pre>@article{dickson2014lipid14, title={Lipid14: the amber lipid force field}, author={Dickson, Callum J and Madej, Benjamin D and Skjevik, {\AA}ge A and Betz, Robin M and Teigen, Knut and Gould, Ian R and Walker, Ross C}, journal={Journal of chemical theory and computation}, volume={10}, number={2}, pages={865--879}, year={2014}, publisher={ACS Publications} }</pre> <p>The trajectories are centered such that the center of mass of the lipid tails are at the origin. <strong>Please check the imaging again to make sure that there are no problems. </strong></p> <p><strong>The trajectories do not contain water molecules.</strong> </p> <p>Simulation Details:</p> <p>Lipids : 72 POPC lipids, 36 per leaflet</p> <p>Water: 9560 TIP3P water molecules (<strong>water coordinates are not saved</strong>)</p> <p>Temperature: 303 K</p> <p>Pressure: 1 bar</p> <p>Thermostat: Langevin</p> <p>Barostat: Berendsen</p> <p>Pressure coupling: Semi-isotropic</p> <p>Trajectory Length: 100 ns (after 100 ns pre-equilibration)</p> <p>Saving frequency: 100 ps</p> <p>Further details are available at the 04_Run.in file</p> <p>All trajectories started from the same structure but equilibriated for 100 ns independently (using 03_Hold.in)</p>
MD simulation trajectory and related files for POPC bilayer in low hydration (Berger model delivered by Tieleman, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation in low hydration (7 water per lipid molecule) ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) with fixed double bond dihedrals, 60ns, T=298K, 128 POPC molecules, 896 water molecules. This data is used in the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite the nmrlipids.blogspot.fi project and the original publications related to the force field.</p>
MD simulation trajectory and related files for POPC bilayer in low hydration (GAFFlipid, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, GAFFlipid force field (http://dx.doi.org/10.1039/C2SM26007G) in low hydration, 40ns, T=303K, 126 POPC molecules, 896 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters: Dickson et al. Soft Matter, 2012,8, 9617-9627 http://dx.doi.org/10.1039/C2SM26007G.</p>
MD simulation trajectory and related files for POPC bilayer (Lipid14, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Lipid14 force field (http://dx.doi.org/10.1021/ct4010307), 50ns, T=303K, 72 POPC molecules, 2234 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project.</p>
MD simulation trajectory and related files for POPC bilayer, Högberg et al parameters (J.Comp.Chem., 29, 2359 (2008))
<p>MD simulation trajectory and related files for POPC bilayer,<br /> A.L.Rabinovich, A.P.Lyubartsev, Journal of Physics: Conference series, 510, 012022 (2014)</p> <p>20 ns( excluded) + 80 ns trajectory<br /> T=303K, 128 lipids + 3840 H2O</p> <p>Force field: from Högberg et al, J.Comp.Chem., 29, 2359 (2008)</p> <p>Software: MDynaMix v 5.2</p> <p>Relevant files:</p> <p>md.input : main MD input file</p> <p>160181_pc.mmol : lipid topology/force field file<br /> H2O.mmol : SPC water</p> <p>ord_160181.in : Input for the analysis utility to extract order parameters</p> <p>Trajectory:</p> <p>160181_pc_mem.102 - 160181_pc_mem.501 - trajectory files, 200 frames / 200 ps in each</p>
POPC_AMBER_LIPID14_NaCl_1Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 1M NaCl. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 77 Na, 77 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
POPC_AMBER_LIPID14_CaCl2_1Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 1M CaCl2. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 100 Ca, 200 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p>
POPC_CHARMM36_CaCl2_035Mol
<p>The starting structure was constructed using the CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/) online tool.</p> <p>All runs were performed with Gromacs 5.0.4 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 35 Ca, 70 Cl. 200ns trajectory (preceded by standard CHARMM-GUI NPT equilibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from 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> <p> </p>
POPC_Ulmschneider_OPLS_NaCl_015Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.15M NaCl. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Ions were described by OPLS-AA force field (Gromacs 5.0.3). Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 12 Na, 12 Cl. 200ns trajectory (preceded by 5ns NPT equillibration).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p>
POPC_Ulmschneider_OPLS_Verlet_Group
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer run with Verlet and Group schemes. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters. 200ns trajectory (preceded by 5ns NPT equillibration). Starting structure was obtained from CHARMM-GUI [3].</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p> <p>[3] http://www.charmm-gui.org/</p>
POPC_AMBER_LIPID14_NaCl_015Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.15M NaCl. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 12 Na, 12 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
POPC_Ulmschneider_OPLS_NaCl_1Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 1M NaCl. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Ions were described by OPLS-AA force field (Gromacs 5.0.3). Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 77 Na, 77 Cl. 200ns trajectory (preceded by 5ns NPT equillibration).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p>
POPC_AMBER_LIPID14_Verlet
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with runned with Verlet scheme. The LIPID14 force field was used with Gromacs 5.0.3. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
POPC_CHARMM36_CaCl2_067Mol
<p>The starting structure was constructed using the CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/) online tool.</p> <p>All runs were performed with Gromacs 5.0.4 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 67 Ca, 134 Cl. 200ns trajectory (preceded by standard CHARMM-GUI NPT equilibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from 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> <p> </p>
POPC_CHARMM36_CaCl2_1Mol
<p>The starting structure was constructed using the CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/) online tool.</p> <p>All runs were performed with Gromacs 5.0.4 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 100 Ca, 200 Cl. 200ns trajectory (preceded by standard CHARMM-GUI NPT equilibration) (2 files of 100ns).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from 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> <p> </p>
POPC_AMBER_LIPID14_CaCl2_035Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.35M CaCl2. The LIPID14 force field was used with Gromacs 5.0.3. Ions were described by AMBER99SB-ILDN force field. Conditions: T=298.15, 128 POPC molecules, 6400 tip3p waters (lipid/water 1:50), 35 Ca, 70 Cl. 200ns trajectory (preceded by 5ns NPT equillibration) (2 files of 100ns).</p> <p>THE TRAJECTORY "035M_CaCl2_POPC_AMB_100_200ns.xtc" IS CORRUPTED. FOR THE UNCORRUPTED FILE PLEASE FOLLOW THE LINK: https://zenodo.org/record/46234</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
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