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158 results for “Charmm36”
POPC with 40 and 50 mol-% of cholesterol at 310 K. Charmm36 force field.
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 40% (134 molecules) and 50 % (200 molecules) of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</p>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 0% (0 molecules), 10 % (22 molecules), 20 % (50 molecules), or 30 % (86 molecules) of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p>*** IMPORTANT ***</p> <p>This is a correction to an earlier dataset simulated with some missing dihedrals, see: DOI: 10.5281/zenodo.61649</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</p>
CHARMM36, NB-Fix approaches, without NBFIX, POPC membrane, Ca, Na ions,
<p>Different versions of NB-Fix from CHARMM-Gui and simulations without NB-Fix (called original charmm)</p> <p>200 POPC lipids, TIP3P - charrmm water model,</p> <p> </p>
MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"
<p>Input files and trajectories of n-alkane/lipid systems used in the article: ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids".</p> <p>Equilibrated starting configurations were created using CHARMM36. Otherwise, filenames specifiy the force field used (C36 or SL), Temperature and system composition.</p> <p>.xtc trajectories were created using gmx trjconv with options -pbc nojump -dt 10. run2 equals simulations from 100-200ns, run3 equals 200-300ns. The first 100ns were excluded from the analysis and are not included in this dataset.</p> <p>Exemplary .mdp files have been included for both force-fields. Please refer to the manuscript for the force field sources and additional information.</p>
Pure POPC bilayer MD simulations with CHARMM36 force field with GROMACS_v2019
<p>500 ns MD simulation of POPC bilayer with CHARMM36 force field at 300 K generated with GROMACS 2019 simulation engine. The system contains 100 POPC lipids per leaflet (200 in total) and 2000 TIP3P water molecules. No, NaCl in the system. This data set contains 500 ns data with 50000 frames (saving frequency is every 10 ps). </p>
NAMD Simulation of Pure POPC Membranes with CHARMM36 Force Field
<p><strong>System:</strong> POPC membrane with 72 (36 x 36) lipids</p> <p><strong>Number of POPC: </strong>72</p> <p><strong>Number of Waters:</strong> 2520</p> <p><strong>Water model: </strong>TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Force Field:</strong> CHARMM36</p> <p><strong>Simulation engine:</strong> NAMD Git-2020-02-27 for Linux-x86_64-multicore-CUDA [Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)]</p> <p><strong>Number of independent repeats per setup: </strong>1.<br> <strong>Trajectory lengths per repeat:</strong> 100 ns.<br> <strong>Previously equilibrated for:</strong> 0 ns.<br> <strong>Sampling rate:</strong> every 100 ps.</p> <p><strong>Time integration step:</strong> 2 fs. (For further info, please see the .inp file)</p> <p> </p> <p> </p>
OpenFF anneal + Lipid21 anneal + CHARMM36 full
Open the record for dataset details and reuse information.
OpenFF w/ MD Integrator + CHARMM36 control w/o HMR + Lipid21 verification w/o HMR
Open the record for dataset details and reuse information.
OpenFF: Lipid21 & CHARMM36 Analyses
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MD simulations of the Sec61/TRAP/ribosome complex and various subcomplexes with CHARMM36 force field
<p>Simulation data for the Sec61/TRAP/ribosome complex and its subcomplexes (TRAP alone, Sec61 alone, as well as Sec61 with TRAP) embedded in an ER membrane mimic. Simulations are performed using GROMACS and with the all-atom CHARMM family of force fields. The uploaded trajectories (xtc) contain the coordinates stored every 2 ns of the 2-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 2 µs are provided. </p> <p>This upload also contains data for the Sec61/TRAP/ribosome complex simulated in a POPC bicelle. This simulation is 1 µs long and the coordinates are stored every 1 ns.</p> <p>All required input files are also provided to regenerate the run input file: initial structures (gro), index files (ndx), topologies (top and itp), and the simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p> <p> </p>
POPC:POPG 4:1 MD simulation with CHARMM36 in 0.1 M CaCL2 solution with Na+ counter ions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions, 26280 TIP3 water molecules, 47 Ca2+ ions and 94 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 1:1 MD simulation with CHARMM36 in 1 M CaCL solution and Na+ counter ions
<p>CHARMM36 POPC:POPG 1:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 150 POPC, 150 POPG, 150 sodium ions, 29766 TIP3 water molecules, 578 Ca2+ ions and 1156 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-400ns.xtc is 20 ps.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in 1 M CaCL2 solution with Na+ counterions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions, 24927 TIP3 water molecules, 451 Ca2+ ions and 902 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 1:1 MD simulation with CHARMM36 in water and Na+ counter ions
<p>CHARMM36 POPC:POPG 1:1 bilayer simulation in water. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 150 POPC, 150 POPG, 150 sodium ions and 31500 TIP3 water molecules.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in water with Na+ counter ions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in water. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions and 26280 TIP3P water molecules.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 1:1 MD simulation with CHARMM36 in 0.1 M CaCL solution and Na+ counter ions
<p>CHARMM36 POPC:POPG 1:1 bilayer simulation in 0.1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 150 POPC, 150 POPG, 150 sodium ions, 31329 TIP3 water molecules, 57 Ca2+ ions and 114 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-400ns.xtc is 20 ps.</p>
POPC CHARMM36 T313K
<p>POPC CHARMM36 T313K. The simulations are ran for simulations with cationic surfactants for NMRlipids IV project at 313 K using Gromacs 5.</p> <p>itp files called in top files can be found from the root of repository https://doi.org/10.5281/zenodo.1288296.</p>
MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, Gromacs 5.1)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 5.1.2 with CHARMM36 lipid forcefield.<br> The simulation is composed of 128 POPC at full hydratation and ran for 500ns at 303K, data saved every 10ps.<br> This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
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