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Dataset results
299 results for “MD simulations”
MacRog POPC/POPE 1:1 MD simulation (300 K - 500ns - 1 bar)
<p>MacRog POPC/POPE 1:1 bilayer simulation. Starting structure from CHARMM-GUI: the initial PDB file was modified to match MacRog nomenclature and atom order. Temperature was set to 300 K and pressure to 1 bar with 128 lipids fully hydrated: 40 water molecules per lipid. The trajectory contains the whole simulation from 0 to 500 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 200-500 ns).</p> <p>The popc.itp and pope.itp files were obtained from the paper doi : 10.1016/j.dib.2016.03.067. Several corrections have been made to the original files (for more information, go check <a href="https://www.dsimb.inserm.fr/~fuchs/project_Samuli/POPC_POPE/report_results_comparison.pdf">https://www.dsimb.inserm.fr/~fuchs/project_Samuli/POPC_POPE/report_results_comparison.pdf</a>). We provide here the corrected itp files.</p>
MD simulation of HpTonB(30-285) in 150mM NaCl with Amber ff03ws force field
<p>MD simulation of periplasmic part of TonB protein from <em>Helicobacter Pylori</em> HpTonB(30-285) with Amber ff03ws force field with 150 mM NaCl. Trajectory contains the last 1000ns of the simulation.</p> <p>micro_nojump_nowater.xtc (10 ps saving frequency), nowater.tpr, and confENDprot.gro contain only protein.</p> <p>1microsecondSKIP.xtc (100 ps saving frequency), md.tpr and confEND.gro contain also solvent.</p> <p>Force field parameters for proteins and counterions are dowloaded from https://github.com/bestlab/force_fields, for NaCl from https://bitbucket.org/hseara/ions</p>
MD simulation of HpTonB(30-285) in 40mM NaCl with Amber ff03ws force field
<p>MD simulation of periplasmic part of TonB protein from <em>Helicobacter Pylori</em> HpTonB(30-285) with Amber ff03ws force field with 40 mM NaCl. Trajectory contains the last 1000ns of the simulation.</p> <p>nojump_nowater.xtc (10 ps saving frequency), md_noSOL.tpr, and confENDprot.gro contain only protein.</p> <p>micro_40mMNaClskip.xtc (100 ps saving frequency), md.tpr and confEND.gro contain also solvent.</p> <p>Force field parameters for proteins and counterions are dowloaded from https://github.com/bestlab/force_fields, for NaCl from https://bitbucket.org/hseara/ions</p>
LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 1000mM CaCl2, 298K
<p>The last 200ns of 720ns of MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 50:50 (150 POPC, 150 POPG) with Na+ counterions and 1000mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPC lipids to get 50:50 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
MD simulations of bilayers containing POPC and Cholesterol: 120POPC_8CHL_31Nwat_neutral (lipid14)
<p>NMRLipids III CholXray project (nmrlipids.blogspot.fi)</p> <p>Gromacs 5.0.4, lipid14 FF (Madej et al. JPCB 2015, 119, 12424), 1 atm, 303K, 200ns</p> <p>128 lipids (120 POPC, 8 CHL), N_wat/lipid = 31, 28576 Atoms</p>
LIPID17 POPC-POPG 50:50 MD simulation, Na+ counterions and 100mM CaCl2, 298K
<p>The last 198ns of a 718ns MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 50:50 (150 POPC, 150 POPG) with Na+ counterions and 100mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPC lipids to get 50:50 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 1000mM CaCl2, 298K
<p>The last 200ns from a 1200ns MD simulation trajectory with Amber lipid 17. POPC-POPG 80:20 (POPC 350, POPG 88) with Na+ counterions and 1000mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPG lipids to get 80:20 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
3x 1 µs all-atom MD trajectories; AMBER ff15ipq & SPC/Eb; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'
<p>Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).</p> <ul> <li>3 x 1 µs all-atom MD simulations of T4 Lysozyme</li> <li>Force field: AMBER ff15ipq with modified methyl rotation barriers<sup>1</sup></li> <li>Water model: SPC/Eb</li> <li>Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters</li> </ul> <p>Contains:</p> <ul> <li>3 x GROMACS .xtc trajectory files for 3 independent simulations</li> <li>3 x corresponding GROMACS .tpr topology files</li> </ul> <p><sup>1</sup> Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2020). Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. <em>Journal of Chemical Physics</em>, <em>152</em>(8). https://doi.org/10.1063/1.5135379</p>
5x 1 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'
<p>Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).</p> <ul> <li>5 x 1 µs all-atom MD simulations of T4 Lysozyme</li> <li>Force field: AMBER ff99SB*-ILDN with modified methyl rotation barriers<sup>1</sup></li> <li>Water model: TIP4P/2005</li> <li>Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters</li> </ul> <p>Contains:</p> <ul> <li>5 x GROMACS .xtc trajectory files for 5 independent simulations</li> <li>5 x corresponding GROMACS .tpr topology files</li> </ul> <p><sup>1</sup> Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. <em>The Journal of Physical Chemistry B</em>, <em>122</em>(19), 5038–5048. https://doi.org/10.1021/acs.jpcb.8b02769</p>
3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'
<p>Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).</p> <ul> <li>3 x 5 µs all-atom MD simulations of T4 Lysozyme</li> <li>Force field: AMBER ff99SB*-ILDN with modified methyl rotation barriers<sup>1</sup></li> <li>Water model: TIP4P/2005</li> <li>Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters</li> </ul> <p>Contains:</p> <ul> <li>3 x GROMACS .xtc trajectory files for 3 independent simulations</li> <li>3 x corresponding GROMACS .tpr topology files</li> </ul> <p><sup>1</sup> Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. <em>The Journal of Physical Chemistry B</em>, <em>122</em>(19), 5038–5048. https://doi.org/10.1021/acs.jpcb.8b02769</p>
POPG MD simulation with Lipid17 in water with Na+ counter ions
<p>Lipid17 POPG bilayer simulation water. The initial structure was taken from https://zenodo.org/record/3832274#.X0OlNxmEZGE . Temperature is 310 K. The system contains 500 POPG, 500 sodium ions and 25000 TIP3 water molecules.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in 0.1 M CaCL2 solution with Na+ counter ions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in 0.1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions, 26280 TIP3 water molecules, 47 Ca2+ ions and 94 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 1:1 MD simulation with CHARMM36 in 1 M CaCL solution and Na+ counter ions
<p>CHARMM36 POPC:POPG 1:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 150 POPC, 150 POPG, 150 sodium ions, 29766 TIP3 water molecules, 578 Ca2+ ions and 1156 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-400ns.xtc is 20 ps.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in 1 M CaCL2 solution with Na+ counterions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions, 24927 TIP3 water molecules, 451 Ca2+ ions and 902 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
Lipid17ecc POPC:POPG 4:1 MD simulation in water with Na+ counter ions
<p>Lipid17ecc POPC:POPG 4:1 bilayer simulation in water. The initial structure was taken from https://zenodo.org/record/3693681#.X0OY5RmEZGE . Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions and 26265 SPCE water molecules.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 1:1 MD simulation with CHARMM36 in water and Na+ counter ions
<p>CHARMM36 POPC:POPG 1:1 bilayer simulation in water. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 150 POPC, 150 POPG, 150 sodium ions and 31500 TIP3 water molecules.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 4:1 MD simulation with CHARMM36 in water with Na+ counter ions
<p>CHARMM36 POPC:POPG 4:1 bilayer simulation in water. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 sodium ions and 26280 TIP3P water molecules.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-300ns.xtc is 20 ps.</p>
POPC:POPG 1:1 MD simulation with CHARMM36 in 0.1 M CaCL solution and Na+ counter ions
<p>CHARMM36 POPC:POPG 1:1 bilayer simulation in 0.1 M CaCl2 solution. The initial structure was taken from CHARMM-GUI. Temperature is 298 K. The system contains 150 POPC, 150 POPG, 150 sodium ions, 31329 TIP3 water molecules, 57 Ca2+ ions and 114 Cl- ions.</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded. Saving frequency of 100-400ns.xtc is 20 ps.</p>
MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 2 (500-1000ns)</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms), and other files</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl200_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 200 mM</p> <p>Number of cations: 32</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 200 mM CaCl<sub>2</sub> part 1</p>
MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl2 part 2
<p>MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl<sub>2</sub> part 2 (500-1000ns)</p> <p>Dataset contains trajectories (_trj) for the last 500ns of the 1000ns trajectory, topology (-out.cms), and other files.</p> <p>For the ease of the upload, trajectory files (_trj) are divided to 100ns pieces and tarred (named desmond_md_cacl50_x-xns.tar.gz)</p> <p>System: POPC bilayer in water</p> <p>Number of lipids: 200 (100/leaflet)</p> <p>Number of waters: 8880</p> <p>Salt: CaCl<sub>2</sub></p> <p>Concentration: 50 mM</p> <p>Number of cations: 8</p> <p>Simulation time: 1000 ns (in this dataset 500-1000ns)</p> <p>Simulation engine: Desmond 2019-4</p> <p>Temperature: 300 K</p> <p>Related dataset: MD simulation of POPC bilayer with OPLS3e force field, 50 mM CaCl<sub>2</sub> part 1</p>
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