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119 results for “gromacs”
POPC bilayer, 154 mM NaCl ions, prosECCo75 version of CHARMM36 FF, 310K, gromacs 2021.2
<p>Atomistic molecular dynamic simulation of POPC lipid bilayer in 154 mM NaCl water solution.</p> <p>Water model: TIP3P - CHARMM36 version<br> Lipids: prosECCo75 version of CHARMM36<br> Ions: Sodium: Na_s: DOI: 10.1021/acs.jpcb.5b05221 ; Jungwirth2015 ; scaled<br> Chloride: Cl_2s: DOI: 10.1080/00268976.2013.875231 ; Jungwirth2014b ; scaled</p> <p>README.yaml contains info on simulations files, plus basic analysis (headgroup order parameters, area per lipid)</p>
POPC bilayer with 50% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs
<p>POPC bilayer with 50% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 180ns of 200ns long simulation.</p> <p>See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B50%25DHMDMAB/T313K/MODEL_LIPID14</p>
POPC bilayer with 42% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs
<p>POPC bilayer with 42% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 180ns of 200ns long simulation.</p> <p>See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B42%25DHMDMAB/T313K/MODEL_LIPID14</p>
POPC bilayer with 30% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs
<p>POPC bilayer with 30% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 80ns of 100ns long simulation.</p> <p>See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B30%25DHMDMAB/T313K/MODEL_LIPID14</p>
POPC bilayer with 10% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs
<p>POPC bilayer with 10% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 80ns of 100ns long simulation.</p> <p>See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B10%25DHMDMAB/T313K/MODEL_LIPID14</p>
POPC bilayer with 20% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs
<p>POPC bilayer with 20% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. Last 80ns of 100ns long simulation.</p> <p>See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC%2B20%25DHMDMAB/T313K/MODEL_LIPID14</p>
POPG lipid bilayer simulation at T298K ran with MODEL_CHARMM_GUI force field and Gromacs
<p>POPG lipid bilayer simulation at T298K ran 100ns with the force field given by CHARMM gui using Gromacs.</p> <p>118 POPG, 4110 TIP3P and 118 potassium molecules.</p> <p> </p>
POPC bilayer simulated at T313K with the Lipid14 model using Gromacs
<p>POPC bilayer with 50% of dihexadecyldimethylammonium simulated at T313K with the Lipid14 model using Gromacs. 70ns long simulation.</p> <p>See also http://nmrlipids.blogspot.cz/2017/07/quantifying-effect-of-bound-charge-on.html and https://github.com/NMRLipids/MATCH/tree/master/Data/Lipid_Bilayers/POPC/T313K/MODEL_LIPID14</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip3p, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip3p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip4p, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip4p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, OPC4, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, OPC4 water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip3p, 303K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip3p water model at 303K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p> <p> </p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip4p, 303K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip4p water model at 303K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</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>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip4p, 298K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip4p water model at 298K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, OPC4, 310K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, OPC4 water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip4p, 310K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip4p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip3p, 298K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip3p water model at 298K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
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