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158 results for “Charmm36”
CHARMM36 DOPS simulations (versions 1 and 2) 303 K 1.0 nm LJ switching
<p>CHARMM36 DOPS simulations (303 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>
SOPC bilayer, CHARMM36
<p>Simulation of SOPC bilayer with 32 lipids per leavlet for 500ns after minimization and 200ns equilibration. The CHARRM36 forcefield was used.</p>
Saccharide simulations comparing CHARMM36, CHARMM36-NBFIX, and prosECCo75 force fields, part 4/4 after revisions
<p>Free energy of rotation around the glycosidic bond of (1,4)-D-GalA-D-GalA and (1,4)-D-GlcA-D-GlcNAc with three different force fields.</p>
CHARMM36 POPS/POPC simulations (versions 1 and 2) 298 K 1.0 nm LJ switching with Na ions
<p>CHARMM36 mixed POPS and POPC bilayer simulations (298 K, starting structure from the CHARMM-GUI with 22 POPS and 110 POPC lipids) 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. These simulations were performed with Na ions used to neutralise the system.</p>
CHARMM36 POPS/POPC simulations (versions 1 and 2) 298 K 1.0 nm LJ switching with K ions
<p>CHARMM36 mixed POPS and POPC bilayer simulations (298 K, starting structure from the CHARMM-GUI with 22 POPS and 110 POPC lipids) 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. These simulations were performed with K ions used to neutralise the system.</p>
CHARMM36 POPS simulations (versions 1 and 2) 298 K 1.0 nm LJ switching with K ions
<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. These simulations were performed with K ions used to neutralise the system.</p>
Simulation data for CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 940 mM of NaCl. </p> <p>The fifth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 940 mM NaCl. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the default Charmm<br> ion parameters (type SOD) for NaCl. NB-Fix used for sodium.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 370 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Simulation data for CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2 ("NB-Fix" used), 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. </p> <p>The second from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the default Charmm<br> ion parameters (type CAL) for CaCl_2. The new extra nonbonded parameters were used for trating the calcium bonding (NB-Fix)</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 360 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Simulation data for CHARMM36 POPC bilayer, 100 lipids/leaflet, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer without ions with CHARMM36 FF from the CHARMM-Gui. </p> <p>The first from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p> </p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 380 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
CHARMM36 simulations of POPC mixed with cationic surfactant
<p>CHARMM36 simulations of POPC mixed with cationic surfactants. The simulations are ran for NMRlipids IV project at 313 K using Gromacs 5.</p> <p>run10* for 10 mol% of surfactant</p> <p>run20* for 20 mol% of surfactant</p> <p>run30* for 30 mol% of surfactant</p> <p>run50* for 50 mol% of surfactant</p> <p>itp files called in top files from the folder ../47molF/CHARMMfiles/ are here in the root</p> <p> </p>
CHARMM36-UA POPE Simulations (versions 1 and 2) 310 K (NOTE: hexagonal membrane and POPE is called PEUA)
<p>Two CHARMM36-UA POPE bilayer simulations performed using GROMACS 5.0.6 for 200 ns with different starting velocities. Simulations were performed with the standard CHARMM36 settings: a 1.2 nm cut-off with PME for the Coulombic interactions and a 1.2 nm cut-off for the van der Waals interactions with the forces switched off at 1.0 nm. These simulations were performed at 310 K with a 336 hexagonal lipid bilayer. The full trajectories are provided bar the initial 100 ns. The starting structure of the membrane was made by reverse mapping an equilibrated MARTINI POPE bilayer (constructed with the INSANE script).</p>
CHARMM36 POPC/POPE (50%-50%) MD simulation (300 K - 300ns - 1 bar)
<p>CHARMM36 POPC 50% POPE 50% bilayer simulation (300 K, starting structure from CHARMM-GUI with 128 POPC and 128 POPE lipids (64 per leaflet for each species) fully hydrated with 34 water molecules per lipid). The trajectory contains the whole simulation from 0 to 300 ns skipped every 100 ps and centered on the P atoms. No ions were added as there is no charge in the system. This bilayer was used to calculate the order parameter and the area per lipid for the NMRlipids project (on the time window 50-300 ns).</p> <p> </p>
CHARMM36 pure POPC MD simulation (300 K - 300ns - 1 bar)
<p>CHARMM36 POPC pure bilayer simulation (300 K, starting structure from CHARMM-GUI with 256 POPC lipids fully hydrated with 34 water molecules per lipid). The trajectory contains the whole simulation from 0 to 300 ns skipped every 100 ps and centered on the P atoms. No ions were added as there is no charge in the system. This bilayer was used to calculate the order parameter and the area per lipid for the NMRlipids project (on the time window 50-300 ns).</p> <p> </p>
POPC:POPS (5:1) with 890 mM potassium simulation with CHARMM36 at 298K
<p>POPC:POPS (5:1) with 890 mM potassium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4946 water molecules and 79 Na<sup>+ </sup>ions.</p>
POPC:POPS (5:1) with 450 mM potassium simulation with CHARMM36 at 298K
<p>POPC:POPS (5:1) with 450 mM potassium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4926 water molecules and 40 Na<sup>+ </sup>ions.</p>
POPC:POPS (5:1) with 440 mM sodium simulation with CHARMM36 at 298K
<p>POPC:POPS (5:1) with 440 mM sodium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4965 water molecules and 39 Na<sup>+ </sup>ions.</p>
POPC:POPS (5:1) with 890 mM sodium simulation with CHARMM36 at 298K
<p>POPC:POPS (5:1) with 890 mM sodium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4932 water molecules and 79 Na<sup>+ </sup>ions.</p>
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 940 mM of NaC. </p> <p>The sixth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 945 mM NaCl. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for NaCl. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2, 310K, GROMACS 5.1.4
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. </p> <p>The fourth from the set of 6 simulations.</p> <p>The goal was to study the effect of scaling the CHARMM FF on the ion binding.</p> <p>Done for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The scaled ECC-Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the ECC-ions<br> for CaCl_2. The new extra nonbonded parameters (NB-Fix) were removed.</p> <p> </p> <p>The Charmm36 force field parameters were obtained from http://charmm-gui.org/</p> <p>Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89.</p> <p>In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here.</p> <p>This is the same scaling as used for ECC-POPC</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 610 ns long with data saved every 100 ps.</p> <p>the initial structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.1–> (.tpr) and the energy output file <br> (.edr) are provided. </p>
Simulation of a POPE bilayer at 310K with the CHARMM36 force field
<p>A bilayer of 144 POPE lipids (72 per leaflet) simulated in water (40 molecules per lipid) for 500 ns using the CHARMM36 force field [1] using GROMACS v. 2018.6 [2]. Topologies are obtained from CHARMM-GUI [3].</p> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p> <p>[3] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p> </p>
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