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Dataset results
158 results for “Charmm36”
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>
Etidocaine binding to POPC membrane, CHARMM36-SwissParam, 418 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>
Simulations of POPC/cholesterol mixtures at 298 K, three system sizes, CHARMM36
<p>GROMACS input and output files. CHARMM36.</p> <p>Membranes with 64, 256, and 1024 lipids.</p> <p>Version 2: Updated with complete files for CHOL0_small.</p>
SMS binding to POPC membrane, CHARMM36-ProteinFF, 39 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-ParamChem, 69 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> <p>FILES:<br> tpr:<br> GMX_VERSION: gromacs version used for "gmx grompp" creation of *.tpr file at local computer</p> <p> log:<br> GMX_VERSION: gromacs version used for "gmx mdrun" at cluster and read out from *.log file</p>
Etidocaine binding to POPC membrane, CHARMM36-ParamChem, 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
<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>
Dibucaine binding to POPC membrane, CHARMM36-SwissParam, 123 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-ParamChem-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-ParamChem, 34 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> <p>FILES:<br> tpr:<br> GMX_VERSION: gromacs version used for "gmx grompp" creation of *.tpr file at local computer</p> <p> log:<br> GMX_VERSION: gromacs version used for "gmx mdrun" at cluster and read out from *.log file</p>
Etidocaine binding to POPC membrane, CHARMM36-SwissParam, 418 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>
Dibucaine binding to POPC membrane, CHARMM36-SwissParam, 15 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>
Etidocaine binding to POPC membrane, CHARMM36-ParamChem, 200 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>
SMS binding to POPC membrane, CHARMM36-ProteinFF, 41 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>
Etidocaine binding to POPC membrane, CHARMM36-SwissParam, 138 mM, 298 K, 177 600 waters
<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
<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>
CHARMM36 POPS simulations (versions 1 and 2) 298 K 1.0 nm LJ switching
<p>CHARMM36 POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with a 1.0 nm point at which to switch off the van der Waals interactions. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
CHARMM36-UA POPS simulations (versions 1 and 2) 298 K 1.0 nm LJ switching
<p>CHARMM36-UA POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with a 1.0 nm point at which to switch off the van der Waals interactions. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
CHARMM36-UA DOPS simulations (versions 1 and 2) 303 K 1.0 nm LJ switching
<p>CHARMM36-UA DOPS simulations (303 K, starting structure from the CHARMM-GUI with appropriate hydrogen atoms removed) performed with a 1.0 nm point at which to switch off the van der Waals interactions. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
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