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299 results for “MD simulation”
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1- MD simulations
<p>Topology, parameter and coordinates files of the Molecular dynamics (MD) simulations of OR5K1 3D models from AlphaFold 2 (AF2) and Homology Modeling (HM). We used ACEMD3 (v3.5.1) as a molecular engine, CHARMM36 as force field. Three replicas of 100 ns (dcd files) for both systems are reported. Water molecules, ions, and membrane atoms (POPC: phosphatidylcholine) atoms were removed from the original trajectories before the upload.</p>
Input files for the MD simulations and free energy calculations for the article "Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions"
<p>Article:<em> </em><a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04818">J. Phys. Chem. B. 125, 9357–9371 (2021) [DOI: 10.1021/acs.jpcb.1c04818]</a></p> <p>The structures of the homopolymers and copolymers simulated are shown in Figures 1 and S1 and Tables 2 and 3. All-atom MD simulation was carried out using GROMACS, and this repository provides the input files with the GAFF/RESP force and initial coordinate files. The free energy of water dissolution was obtained with <a href="https://sourceforge.net/projects/ermod/">ERmod</a>, and the input files for the free-energy calculations are also contained. See the README files for details.</p>
MD simulation of sphingomyelin (d18:1/18:0) bilayer in water
<p>MD simulations of sphingomyelin (d18:1/18:0) bilayer in water, NPT, 328 K. 128 SM + 5120 TIP3P water molecules, CHARMM36 force field.</p>
All-atom MD simulations of POPC/SSM/CHOL mixture
<p>All-atom MD simulation of lipid bilayer in water, with composition POPC/SSM/CHOL, at 321.15 K, NPT conditions.</p> <p>Force field: CHARMM36. Water model: TIP3P. Number of molecules: 100 POPC + 100 SSM + 100 CHOL + 9000 SOL + 18 Na+ + 18 Cl-.</p> <p>SSM is (d18:1/18:0) sphingomyelin.</p> <p>Duration of the simulation: 300 ns.</p>
MD Simulations HsGluN1/GluN2A WT/F553A
<p>Molecular dynamics simulation of the HsGluN1/GluN2A WT and F553A (GluN2A) mutant.</p> <p> </p> <p>HsGluN12AA_used_1.pdb is the full-length model that was used for the simulations following truncation of the ATDs.</p> <p> </p> <p>This dataset is from "NMDA Receptor Channel Gating Control by the Pre-M1 Helix<strong>" </strong>by Miranda J. McDaniel, Kevin K. Ogden, Steven A. Kell, Pieter B. Burger, Dennis C. Liotta, and Stephen F. Traynelis (2020).</p>
MacRog pure POPE MD simulation (300 K - 500ns - 1 bar)
<p>MacRog POPE 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 POPE 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 pope.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>
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>
QM/MM MD simulations of the ES complexes of SARS-CoV-2 main protease and oligopeptide substrates
<p>qmdcd.7z : QM/MM MD trajectories for all considered systems in dcd format for QM parts without link atoms (QMpart_nolink.pdb)</p> <p>frames.7z : QM parts of the MD frames selected for the electron density analysis.</p> <p> </p> <p> </p>
Dataset to reproduce MD simulations described in " Insights on the dynamics of the human zinc transporter ZnT8 by MD simulations"
<p>Second version includes full length 6xpf-based models and corresponding MD simulations.</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 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 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>
MD simulation trajectory and related files for DMPC bilayer, Högberg et al, J.Comp.Chem., 29, 2359 (2008)
<p>MD simulation trajectory and related files for DMPC bilayer, from paper: C.J.Högberg, A.M,Nikitin, A.P.Lyubartsev, J.Comp.Chem., 29, 2359 (2008)</p> <p>25ns( excluded) + 55 ns trajectory<br /> T=303K, 98 lipids + 2700 H2O<br /> software: MDynaMix v 5.0</p> <p>Relevant files:</p> <p>md.input : main MD input file</p> <p>dmpc_2008.mmol : lipid topology/force field file<br /> H2O.mmol : SPC water</p> <p>order.in : Input for the analysis utility to extract order parameters</p> <p>Trajectory files:</p> <p>dmpc_NewMod.250 - dmpc_NewMod.849</p> <p>Most of files contain 100 frames taken with 1 ps interval</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>
MD simulation trajectory of a lipid bilayer: 70/30 mol% POPC/Cholesterol . SLIPIDS, Gromacs 4.6.3. 2016.
<p>MD simulation trajectory files, for fully hydrated POPC + CHOLESTEROL bilayer (70/30 mol%) [358 POPC, 154 CHOL, 21183 WAT]. The SLIPIDS force field was used with Gromacs 4.6.3. Conditions: T=298K. 170 ns each trajectory, last 100 ns analyzed.</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>
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