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158 results for “Charmm36”
Simulation of DMPS monolayer (CHARMM36, apl 36/45 A2, 50 mM)
<p>FF: CHARMM36<br>Engine: GROMACS 5.1.4</p> <p><strong>36A^2</strong></p> <p>Preequilibration: 300 ns.<br>Trajectory length: 200 ns</p> <p>System: 100 DMPS + 10,000 SOL + 15KCl</p> <p><strong>45A^2</strong></p> <p>Preequilibration: 300 ns.<br>Trajectory length: 250 ns.</p> <p>System: 100 DMPS + 10,000 SOL + 20KCl</p>
Simulation of DMPS monolayer (CHARMM36, apl 70/80 A2, 50 mM)
<p>FF: CHARMM36<br>Engine: GROMACS 5.1.4</p> <p><strong>70A^2</strong></p> <p>Preequilibration: 0 ns.<br>Trajectory length: 400+ ns</p> <p>System: 100 DMPS + 10,000 SOL + 10KCl</p> <p><strong>80A^2</strong></p> <p>Preequilibration: 0 ns.<br>Trajectory length: 400+ ns.</p> <p>System: 100 DMPS + 10,000 SOL + 10KCl</p>
MD Simulation of AtALMT9 TMD Using Martini3 and charmm36 Force Field
<p>This dataset contains the MD simulation data associated with the article:</p> <p>"Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9"</p> <p><em>(Not published yet)</em></p> <p> </p> <p>Folder</p> <p>AA : All-atom simulation files.</p> <p>CG : Coarse-grained simulation files.</p> <p>toppar : parameter files.</p> <p> </p> <p>File Description</p> <p>conf.pdb : Initial structure of the simulation.</p> <p>all.fit.10ns.now.zen.xtc : trajectory file without water. </p> <p>now.pdb : coordinate file of corresponding trajectory.</p> <p>topol.top : GROMACS topology file.</p> <p> </p> <p> </p>
Set simulations small pure bilayers with cholesterol (max 128 lipids) using charmm36 ff in gromacs (DPPC)
<p>Collection simulations of small pure bilayers (max 128 phospholipids) with cholesterol in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <ol> <li>DPPC_128_CHL1_32_310K</li> </ol> <p>For further information read the Readme file provided for each simulation.</p>
Simulations POPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of POPC (512 lipids) bilayers in gromacs using the charmm36 force field. The list of systems can be found below where the several parameter are:</p> <ol> <li>POPC_512_310K (500ns)</li> <li>POPC_512_NaCl_150mM_310K (500ns)</li> <li>POPC_512_NaCl_150mM_310K_tip3p (500ns)</li> <li>POPC_512_NaCl_Dang_150mM_310K (500ns)</li> </ol> <p>For further information read the Readme file provided for each simulation.</p>
MD simulations of bOG:DMPC in CHARMM36 force field
<p>CHARMM-GUI based series of simulations of beta-octyl-D-glucopyranoside (b-OG) mixed with DMPC at different dilutions. bOG:DMPC mol ratios are 1:1, 1:2, and 2:3. The only change in the force field was changing atom names from 2H2 to H2 in BOG residue to allow **gmx grompp** to recognize protons as protons when setting up constraints for bonds with hydrogens.</p> <p>Simulations are performed in highly hydrated state. I can name it "more than 50 water per two acyl chains"; "water per lipid" measure doesn't work here because bOG has just a single hydrocarbon tail.</p> <p>Trajectory length: 500 ns (20 ps step). T = 303 K. </p> <p>In this version we add *znd files where atom names are unique (changed in a new version of BOG.itp).</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>
MD simulation trajectory and related files for DPPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field (dx.doi.org/10.1021/jp101759q), 25ns, T=323K, 72 POPC molecules, 2189 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 (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectories of Glycerol for different POPC/Cholesterol concentrations (0,10,15,20,25,35,50%). CHARMM36, Gromacs 4.6.3. 2014.
<p>MD simulation trajectories files, for fully hydrated POPC + CHOLESTEROL bilayer. The CHARMM36 force field was used with Gromacs 4.6.3. Conditions: T=298K and different cholesterol concentrations described in the name of each file. 170 ns each trajectory, last 100 ns analyzed.</p> <p> </p>
Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014
<p>MD simulation files</p> <p>72 hydrated DPPC + 2189 water TIP3P </p> <p>NPgT</p> <p>P=1atm, gamma=0, T=323K (liquid crystalline phase)</p> <p>20 ns equilibration (not here)</p> <p>50 ns trajectory (dcd file)</p> <p>Model : Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 United Atom Chain Model for Lipids and Surfactants. <em>J Phys Chem B</em>. 2014;118(2):547-556. doi:10.1021/jp410344g.</p> <p>----<br /> * bilayer-72DPPC-c36-AU.psf : NAMD2.10 structure file Obtained with psfgen utility, using</p> <p>1) topology from Lee et al. 2014</p> <p>2) positions from J. Klauda.</p> <p>http://terpconnect.umd.edu/~jbklauda/research/download.html</p> <p>----</p> <p>* dppc_c36_AU.equil.2.dcd : trajectory file of 2635 frames every 20 ps.</p> <p>---<br /> * measure_SCD_heads.tcl : file used to measure order parameters for the head hydrogens using vmd-1.9</p> <p>---</p> <p>*namd_input.tar files usefull to launch the simulations using NAMD(2.10).</p>
Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014
<p>MD simulation files</p> <p>72 hydrated DPPC + 2189 water TIP3P </p> <p>NPgT</p> <p>P=1atm, gamma=0, T=323K (liquid crystalline phase)</p> <p>20 ns equilibration (not here)</p> <p>50 ns trajectory (dcd file)</p> <p>Model : Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 United Atom Chain Model for Lipids and Surfactants. <em>J Phys Chem B</em>. 2014;118(2):547-556. doi:10.1021/jp410344g.</p> <p>----<br /> * bilayer-72DPPC-c36-AU.psf : NAMD2.10 structure file Obtained with psfgen utility, using</p> <p>1) topology from Lee et al. 2014</p> <p>2) positions from J. Klauda.</p> <p>http://terpconnect.umd.edu/~jbklauda/research/download.html</p> <p>----</p> <p>* dppc_c36_AU.equil.2.dcd : trajectory file of 2635 frames every 20 ps.</p> <p>---<br /> * measure_SCD_heads.tcl : file used to measure order parameters for the head hydrogens using vmd-1.9</p> <p>---</p> <p>*namd_input.tar files usefull to launch the simulations using NAMD(2.10).<br /> </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_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 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 lipid membrane, 303K, Charmm36 force field, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<p>POPC lipid membrane, 303K, Charmm36 force field, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2</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 Gromacs 5.1.2 software package 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>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 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<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 Gromacs 5.1.2 software package 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, 200ns 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, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<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 Gromacs 5.1.2 software package 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>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>
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