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56 results for “dppc”
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>
DPPC bilayer after 100 ns
<p>Equilibrated system of 128 DPPC lipids and 3655 water molecules after 100 ns.</p> <p><strong>Details:</strong> Berger united atom lipids (needs lipid.itp and dppc.itp from Peter Tieleman's web site at <a href="http://moose.bio.ucalgary.ca/">http://moose.bio.ucalgary.ca/</a>). Area per lipid: 0.645 (+/- 0.010) nm<sup>2</sup>.</p> <p>Also available at: <a href="http://www.softsimu.net/downloads.shtml">http://www.softsimu.net/downloads.shtml</a></p> <p><strong>References:</strong></p> <ol> <li><a href="http://dx.doi.org/10.1016/S0006-3495(03)75094-2">Major artifacts due to truncating electrostatic interactions</a>, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, Peter Lindqvist, and Ilpo Vattulainen, Biophys. J. 84, 3636-3645 (2003)</li> <li><a href="http://dx.doi.org/10.1021/jp031281a">Lipid bilayers driven to a wrong lane in molecular dynamics simulations by truncation of long-range electrostatic interactions</a>, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen, J. Phys. Chem. B 108, 4485-4494 (2004).</li> </ol>
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>
DPPC_Berger_NaCl_scaled
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 150 mM NaCl. Berger-DPPC-98 force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) was used with Gromacs 5.0.4. Ions were described by the gromos force field. Ion charges were scaled by a factor 0.7. Conditions: T=323K, 72 lipids, 2880 SPC waters, 8 Na, 8 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_Berger_NaCl
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 150 mM NaCl. Berger-DPPC-98 force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) was used with Gromacs 5.0.4. Ions were described by the gromos force field. Conditions: T=323K, 72 lipids, 2880 SPC waters, 8 Na, 8 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_512_NaCl_150mM_320K
<p>System description<br /> -------------------<br /> - Title: Simulation DPPC_512_NaCl_150mM_320K bilayer<br /> <br /> - MD engine: gromacs 5.0.4<br /> <br /> - Force field: charmm36<br /> <br /> - Temperature: 320K<br /> <br /> - Simulation time: 700ns<br /> <br /> - Saving frequency: 100ps <br /> <br /> - Molecular content:<br /> DPPC 512<br /> water 20480<br /> Cl- 55<br /> Na+ 55<br /> <br /> - Other information:<br /> * Center of mass motion removed independently for bilayer and water+ions<br /> </p>
DPPC_Berger_OPLS06_NaCl_scaled
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 150 mM NaCl. The OPLS-AA-compatible Berger-DPPC-06 force field (DOI:10.1088/0953--8984/18/28/S07) was used with Gromacs 4.6.7. Ions were described by the Åqvist parameters. The ion charges were scaled by a factor 0.7. Conditions: T=323K, 72 lipids, 2880 SPC waters, 8 Na, 8 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_Berger_OPLS06_NaCl
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 150 mM NaCl. The OPLSAA-compatible Berger-DPPC-06 force field (DOI:10.1088/0953--8984/18/28/S07) was used with Gromacs 4.6.7. Ions were described by the Åqvist parameters. Conditions: T=323K, 72 lipids, 2880 SPC waters, 8 Na, 8 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_Berger_OPLS06_NaCl_1Mol_scaled
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 1 M NaCl. The OPLS-AA-compatible Berger-DPPC-06 force field (DOI:10.1088/0953--8984/18/28/S07) was used with Gromacs 5.0.4. Ions were described by the Åqvist parameters. The ion charges were scaled by a factor 0.7. Conditions: T=323K, 72 lipids, 2778 SPC waters, 51 Na, 51 Cl. 120 ns trajectory, last 60 ns analyzed.</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>
DPPC_Berger_NaCl_1Mol
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 1 M NaCl. Berger-DPPC-98 force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) was used with Gromacs 5.0.4. Ions were described by the gromos force field. Conditions: T=323K, 72 lipids, 2778 SPC waters, 51 Na, 51 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_Berger_OPLS06_NaCl_1Mol
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 1 M NaCl. The OPLSAA-compatible Berger-DPPC-06 force field (DOI:10.1088/0953--8984/18/28/S07) was used with Gromacs 5.0.4. Ions were described by the Åqvist parameters. Conditions: T=323K, 72 lipids, 2778 SPC waters, 51 Na, 51 Cl. 120 ns trajectory, last 60 ns analyzed.</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>
DPPC_Berger_NaCl_1Mol_scaled
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 1 M NaCl. Berger-DPPC-98 force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) was used with Gromacs 5.0.4. Ions were described by the gromos force field. Ion charges were scaled by a factor 0.7. Conditions: T=323K, 72 lipids, 2778 SPC waters, 51 Na, 51 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
DPPC_512_325K
<p>System description<br /> -------------------<br /> - Title: Simulation DPPC_512_325K bilayer<br /> <br /> - MD engine: gromacs 5.0.4<br /> <br /> - Force field: charmm36<br /> <br /> - Temperature: 325K<br /> <br /> - Simulation time: 500ns<br /> <br /> - Saving frequency: 100ps <br /> <br /> - Molecular content:<br /> DPPC 512<br /> water 20480<br /> <br /> - Other information:<br /> * Center of mass motion removed independently for bilayer and water<br /> </p>
DPPC_512_NaCl_150mM_320K_v-rescale
<p>System description<br> -------------------<br> - Title: Simulation DPPC_512_NaCl_150mM_320K_v-rescale bilayer<br> <br> - MD engine: gromacs 5.0.4<br> <br> - Force field: charmm36<br> <br> - Temperature: 320K<br> <br> - Simulation time: 500ns<br> <br> - Saving frequency: 100ps <br> <br> - Molecular content:<br> DPPC 512<br> water 20480<br> Cl- 55<br> Na+ 55<br> <br> - Other information:<br> * Use of v-rescale thermostat instead of the default nose-hoover<br> * Center of mass motion removed independently for bilayer and water+ions<br> </p>
DPPC_Berger_OPLS06_NaCl_1Mol
<p>MD simulation trajectory and related files for fully hydrated DPPC bilayer with 1 M NaCl. The OPLSAA-compatible Berger-DPPC-06 force field (DOI:10.1088/0953--8984/18/28/S07) was used with Gromacs 5.0.4. Ions were described by the Åqvist parameters. Conditions: T=323K, 72 lipids, 2778 SPC waters, 51 Na, 51 Cl. 120 ns trajectory, last 60 ns analyzed.</p>
Simulations DPPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DPPC (512 lipids) bilayers in gromacs using the charmm36 force field. Several temperatures between 315 and 338 K are included. The list of systems can be found below where the several parameter are:</p> <p>1) DPPC_512_NaCl_150mM_315K_v-rescale (500ns)<br> 2) DPPC_512_NaCl_150mM_320K (700ns)<br> 3) DPPC_512_NaCl_150mM_320K_v-rescale (500ns)<br> 4) DPPC_512_NaCl_150mM_322K_v-rescale (700ns)<br> 5) DPPC_512_NaCl_150mM_325K (500ns)<br> 6) DPPC_512_NaCl_150mM_325K_v-rescale (500ns)<br> 7) DPPC_512_NaCl_150mM_325K_cutoff09 (500ns)<br> 8) DPPC_512_NaCl_150mM_325K_MEMB_338K (500ns)<br> 9) DPPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Set simulations small pure bilayers (72 lipids) using charmm36 ff in gromacs (DPPC, POPC)
<p>Collection simulations of DPPC and POPC bilayers in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <p>1) DPPC_72_325K (500ns)<br> 2) DPPC_72_310K_rmcomm_leaflets (500ns)<br> 3) DPPC_72_310K_rmcomm_leaflets_low_hydration (500ns)<br> 4) POPC_72_310K (500ns)<br> 5) POPC_72_310K_rmcomm_leaflets (500ns)<br> 6) POPC_72_310K_rmcomm_leaflets_low_hydration (550ns)<br> 7) POPC_72_303K_rmcomm_leaflets_low_hydration (550ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
DPPC lipid bilayer simulation with CHARMM36-LJPME force field using OpenMM
<p>DPPC lipid bilayer simulation (300 ns) with CHARMM36-LJPME force field using OpenMM at 323K.</p> <p>Used in <a href="http://doi.org/10.1021/acs.jctc.1c00951">https://doi.org/10.1021/acs.jctc.1c00951</a></p> <p>The force field parameters were downloaded from <a href="https://terpconnect.umd.edu/%7Ejbklauda/ff.html">https://terpconnect.umd.edu/%7Ejbklauda/ff.html</a>.</p> <p><a href="https://zenodo.org/api/files/1e89f677-91a8-472d-aebb-144fddd58d23/trajCORRECT1-2.dcd?versionId=5317fd88-6b98-4905-b171-53c1cd199cfe">trajCORRECT1-2.dcd </a>has incorrect timestamps. traj1-2.xtc has correct timestamps.<br> </p>
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