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36 results for “Charmm36, POPC, membrane”
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>
Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine
<p>Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine</p> <p>NaCl concentration is 730 mM.</p> <p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
TPP binding to POPC membrane, CHARMM36-QMcharges, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-ProteinFF, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-ProteinFF-ECC, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-ProteinFF, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-ProteinFF-ECC, 416 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature-ECC, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature-ECC, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature, 416 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-ECC, 416 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-ECC, 277 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
Etidocaine binding to POPC membrane, CHARMM36-SwissParam, 138 mM, 298 K, started from overbound
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-Literature-ECC, 416 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
TPP binding to POPC membrane, CHARMM36-QMcharges-ECC, 138 mM, 298 K
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
Etidocaine binding to POPC membrane, CHARMM36-SwissParam, 280 mM, 298 K, started from overbound
<p>System info in README.yaml, including basic analysis - headgroup OP, averaged APL and repead distance, analysis performed only from eqilibrated part of the simulation, marked as "BINDINGEQ"</p> <p>here:</p> <p>FILES:<br> xtc:<br> NAME: [name]<br> SIZE: [MB]<br> MODIFIED: [yyyy-mm-dd time]<br> LENGTH: [ps]<br> SAVING_FREQUENCY: [ps]<br> BEGIN: [ps] - how much of the simulation was simulated before and is excluded</p>
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