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220 results for “force fields”
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>
POPC with 40 and 50 mol-% of cholesterol at 310 K. Slipids force field.
<p>Simulations of a POPC bilayer with varying amounts of cholesterol. This data is employed for the NMRlipids project, see <em>http://nmrlipids.blogspot.fi</em> for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 40% (134 molecules) or 50 % (200 molecules) of cholesterol. The Slipids model [1–3] is employed for lipids, and the tip3p model for water.</p> <p>The Slipids force field parameters were downloaded from http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), binary run input file for GROMACS v. 4.6–> (.tpr) and the energy output file (.edr) are provided together with the run parameter file (.mdp) employed to run all the simulations.</p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field.
<p>Simulations of a POPC bilayer with varying amounts<br> of cholesterol. This data is employed for the NMRlipids<br> project, see <em>http://nmrlipids.blogspot.fi</em> for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 0% (0 molecules), 10 %<br> (22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br> of cholesterol. The Slipids model [1–3] is employed for lipids,<br> and the tip3p model for water.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. Additionally,<br> the initial structure (.gro), topology (.top), index file (.ndx),<br> binary run input file for GROMACS v. 4.6–> (.tpr) and the<br> energy output file (.edr) are provided together with the run<br> parameter file (.mdp) employed to run all the simulations.</p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl.</p> <p>The numbers in the file names denote the number of additional cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field parameters, SPC/E water model and ECC-ions.</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
The force field, parameters and configurations from the paper "Dispersion of hydrophilic nanoparticles in natural rubber with phospholipids"
<p>The force field, parameters and configurations from the paper "Dispersion of hydrophilic nanoparticles in natural rubber with phospholipids"</p>
Unstable gas flow in a flat channel under the influence of a transverse force field: self-oscillations of the jet
<p>For a description of the task, see the original paper.</p> <div> <div> <div> <div>For each video, there are the meaning of force (F), Section and Subsection of the article where this video is mentioned, as well as the number of Figure from the article corresponding to this calculation. The Mach number is 0.29 for all the calculations.</div> </div> </div> </div> <p>(1) "Video-1.avi": </p> <p>F = 2.5, </p> <p>Section "Main modeling results"</p> <p>Subsection "Weak force field"</p> <p>Figure 2</p> <p> </p> <p>(2) "Video-2.avi": </p> <p>F = 4, </p> <p>Section "Main modeling results"</p> <p>Subsection "Strong force field"</p> <p>Figure 3</p> <p> </p> <p>(3) "Video-3.avi": </p> <p>F = 3, </p> <p>Section "Main modeling results"</p> <p>Subsection "Average force field"</p> <p>Figure 4</p> <p> </p> <p>(4) "Video-4.avi": </p> <p>F = 7 (continuous force field, see Figure 5), </p> <p>Section "Main modeling results"</p> <p>Subsection "Continuous force field"</p> <p>Figure 6</p>
POPS+83%popc lipid bilayer simulation at T298K ran CHARMM_GUI force field and Gromacs
<p>POPS+83%popc lipid bilayer simulation at T298K ran CHARMM_GUI force field and Gromacs. 100ns long trajectory.</p>
OPEPv7 Force Field: Parameters of Non-Bonded Interaction Potentials
<p>Parameters defining interaction potentials between amino-acid beads in the OPEPv7 force field.</p> <p>CA stands for the C<span class="math-tex">\(\alpha\)</span> bead of any residue except for glycine, which has a dedicated bead type, labeled as CAG. The side-chain beads are each named after the corresponding residue.</p> <p>“12-6” represents the Lennard-Jones potential, in which case the <span class="math-tex">\(C_{12}\)</span> and <span class="math-tex">\(C_{6}\)</span> parameters are given in the table. “OPEP” denotes the OPEP side-chain potential with an attractive term while “OPEM” stands for the purely repulsive variant (see <a href="https://doi.org/10.1039/C4CS00048J">Chem. Soc. Rev., 2014,43, 4871-4893</a>). In both cases, the <span class="math-tex">\(r^{0}_{ij}\)</span> and <span class="math-tex">\(\varepsilon_{ij}\)</span> parameters are given.</p> <p>The parameters of the default OPEPv7 force field are listed in the <strong>OPEPv7.dat file</strong>. The <strong>OPEPv7_LJ_fit.dat</strong> file provides a simplified version of the force field where the “OPEP” potentials are replaced by Lennard-Jones fits.</p>
The dataset for "Force-free current sheets in the Jovian magnetodisk: a key role of electron field-aligned anisotropy"
<p>The dataset for "Force-free current sheets in the Jovian magnetodisk: a key role of electron field-aligned anisotropy" submitted to J. Geophys. Res. This dataset contains information about 18 current sheet in the Jovian magnetodisk. PDF file includes the table and eighteen figures with current sheets. The table lists corresponding dates/times of the current sheet crossings by Juno spacecraft. Archive includes ASCII flies with data plotted on these figures.</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>
OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC 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>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872447</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc format
<p>PSF, single CRD file, and XTC format trajectories for the final 200 ns of triplicate POPC simulations, from the publication</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion: 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*</p> <p> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in<span> 10.5281/zenodo.7871949 have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</span></p>
OpenMM simulations of DMPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC 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>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872767</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
OpenMM simulations of DLPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC 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>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872783</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
Pure POPC membrane simulations with 790 mM CaCl2 with the CHARMM-Drude2023 force field (OpenMM)
<p>214.85 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 91 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. Frame saving frequency is 10ps. There are 21485 frames in this trajectory.</p>
Pure POPC membrane simulations with 350 mM NaCl with the CHARMM-Drude2023 force field (OpenMM)
<p>223.97 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 41 NaCl, 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. Frame saving frequency is 10ps. There are 22397 frames in this trajectory.</p>
Active Brownian particles in external force fields: field-theoretical models, generalized barometric law, and programmable density patterns
<p>Supplementary data for the following manuscript: Jens Bickmann, Stephan Bröker, Michael te Vrugt, Raphael Wittkowski, "Active Brownian particles in external force fields: field-theoretical models, generalized barometric law, and programmable density patterns".</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>
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