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8 results for “DEPC”
Simulations of DLPC, DOPC, and DEPC membranes
<p>Simulations of three different lipid bilayers using the CHARMM36 lipid model. The bilayers were built using CHARMM-GUI and simulated for 500 ns using Gromacs 2019. The systems contain 200 lipids (DLPC, DOPC, or DEPC), 50 lipids per water, and 130 mM NaCl. For each simulation, the run input file (tpr), topology (top), index (ndx), trajectory (xtc), log file (log), energy file (edr), continue point (cpt), and the final structure (gro) are given. The topology refers to the Gromacs-compatible CHARMM36 force field, available at http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and to other itp files provided in this upload. The simulation parameters are given in the md.mdp file.</p>
Simulations of GpA-based dimers of various lengths in DEPC, DOPC, and DLPC bilayers, part 2/2
<p>Dimers of transmembrane (TM) peptides based on the Glycophorin A (GpA) dimer are simulated in different membrane environments. Three different homodimers with varying TM domain lengths and one heterodimer are considered. The homodimers are formed of either</p> <ul> <li>17L (GRPNLKLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLEYP)</li> <li>23L (GRPNLKLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLEYP)</li> <li>29L (GRPNLKLLLLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLLLLEYP)</li> </ul> <p>peptides, while the heterodimer consists of one 17L peptide and one 29L peptide. In the sequences, the bold letters denote the amino acids involved in the GpA dimerization motif. The dimers are simulated in DLPC (12:0 PC), DOPC (18:1 PC), or DEPC (22:1 PC) bilayers. Additionally, a polyleucine dimer is simulated in a DOPC bilayer. Bilayers consist of 400 lipids and they are adequately hydrated with 24000 water molecules and 134 mM NaCl. The simulations are 100 ns long with trajectories written every 100 ps.</p> <p>The files are named as XXX-YYYY.ZZZ, where XXX denotes to the peptide type ('het' for the heterodimer and 'polyl' for the polyleucine), YYYY denotes the bilayer type, and ZZZ denotes the file type. Files are in Gromacs format: .xtc for trajectories, .edr for energy data, .cpt for continue points, .ndx for index files, .top for topology files, and .tpr for run input files (Gromacs 5.1). The simulation parameter file (md.mdp) is common for all systems. The CHARMM36 force field is used; topologies are obtained from CHARMM-GUI, and those of the peptides are included in Gromacs format (.itp).</p> <p>More information on the systems is available in the publication, available here: (TO BE INCLUDED!)</p> <p>Note that the data for the homodimers (bar polyleucine) are in part 1/2, available at https://doi.org/10.5281/zenodo.573257</p>
Simulations of GpA-based dimers of various lengths in DEPC, DOPC, and DLPC bilayers, part 1/2
<p>Dimers of transmembrane (TM) peptides based on the Glycophorin A (GpA) dimer are simulated in different membrane environments. Three different homodimers with varying TM domain lengths and one heterodimer are considered. The homodimers are formed of either</p> <ul> <li>17L (GRPNLKLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLEYP)</li> <li>23L (GRPNLKLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLEYP)</li> <li>29L (GRPNLKLLLLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLLLLEYP)</li> </ul> <p>peptides, while the heterodimer consists of one 17L peptide and one 29L peptide. In the sequences, the bold letters denote the amino acids involved in the GpA dimerization motif. The dimers are simulated in DLPC (12:0 PC), DOPC (18:1 PC), or DEPC (22:1 PC) bilayers. Additionally, a polyleucine dimer is simulated in a DOPC bilayer. Bilayers consist of 400 lipids and they are adequately hydrated with 24000 water molecules and 134 mM NaCl. The simulations are 100 ns long with trajectories written every 100 ps.</p> <p>The files are named as XXX-YYYY.ZZZ, where XXX denotes to the peptide type ('het' for the heterodimer and 'polyl' for the polyleucine), YYYY denotes the bilayer type, and ZZZ denotes the file type. Files are in Gromacs format: .xtc for trajectories, .edr for energy data, .cpt for continue points, .ndx for index files, .top for topology files, and .tpr for run input files (Gromacs 5.1). The simulation parameter file (md.mdp) is common for all systems. The CHARMM36 force field is used; topologies are obtained from CHARMM-GUI, and those of the peptides are included in Gromacs format (.itp).</p> <p>More information on the systems is available in the publication, available here: (TO BE INCLUDED!)</p> <p>Note that the data for the heterodimer and for the polyleucine are in part 2/2, available at https://doi.org/10.5281/zenodo.573274</p>
Simulations of a rhomboid protease GlpG in DEPC membranes *OBSOLETE*
<p>both replicas 5 microseconds, C36</p> <p>These simulations are affected by https://redmine.gromacs.org/issues/2845</p>
Simulations of a lactose permease LacY in DEPC membranes
<p>2 replicas, 5 microseconds, C36</p>
Simulations of a rhomboid protease GlpG in DEPC membranes
<p>both replicas 5 microseconds, C36</p>
Simulations of DLPC, DOPC, and DEPC membranes in different sizes
<p>100 and 200 lipids 1 microsecond, 800 lipids 500 ns.</p>
Simulations of a rhomboid protease GlpG with cytosolic domain in DEPC membranes
<p>5 microseconds, C36</p>
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