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Dataset results
4 results for “ULMSCHNEIDER”
POPC_Ulmschneider_OPLS_NaCl_015Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 0.15M NaCl. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Ions were described by OPLS-AA force field (Gromacs 5.0.3). Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 12 Na, 12 Cl. 200ns trajectory (preceded by 5ns NPT equillibration).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p>
POPC_Ulmschneider_OPLS_Verlet_Group
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer run with Verlet and Group schemes. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters. 200ns trajectory (preceded by 5ns NPT equillibration). Starting structure was obtained from CHARMM-GUI [3].</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p> <p>[3] http://www.charmm-gui.org/</p>
POPC_Ulmschneider_OPLS_NaCl_1Mol
<p>MD simulation trajectory and related files for fully hydrated POPC bilayer with 1M NaCl. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Ions were described by OPLS-AA force field (Gromacs 5.0.3). Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters, 77 Na, 77 Cl. 200ns trajectory (preceded by 5ns NPT equillibration).</p> <p>This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p>
POPC @ 310K, Model by Ulmschneider and Ulmschneider
<p>Files required for a simulation of a POPC bilayer and the resulting trajectories. The POPC model is that by Ulmschneider and Ulmschneider [1]. The structure and topology files are downloaded from Lipidbook [2]. The files (xtc and mdp) with '_dc' suffix are simulated with dispersion correction applied to both energy and pressure whereas the files without this suffix do not use this correction.</p> <p>This data is used in the project "Matching lipid force fields with NMR data", see: http://nmrlipids.blogspot.fi </p> <p>[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813</p> <p>[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html</p>
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