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51 results for “CHARMM36m”
CHARMM36M Force Field Parameters for the Thioester Bond between Cysteine and Glycine
<p>CHARMM36M force field parameters for the thioester bond connecting the side chain of a cysteine to the carbonyl of a C-terminal glycine.</p> <p>The dataset includes parameter and auxiliary files in GROMACS format. In addition, a short tutorial shows how to patch the CHARMM36M force field and use the parameters.</p> <p>These parameters have been developed for the parameterization and simulation of the Ubc6 ubiquitin complex, but can be used with any conparable system.</p> <p>Details about the parameterization are provided in:</p> <p><br><a href="https://www.embopress.org/doi/full/10.1038/s44318-024-00301-3">Swarnkar, Anuruti, Florian Leidner, Ashok K. Rout, Sofia Ainatzi, Claudia C. Schmidt, Stefan Becker, Henning Urlaub, Christian Griesinger, Helmut Grubmüller, and Alexander Stein. "Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes." <em>The EMBO Journal</em> (2024): 1-35.</a></p> <p> </p> <p> </p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the third out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
HpTonB(30-285) simulation CHARMM36m
<p>Simulation of periplasmic part of TonB protein from <em>Helicobacter Pylori</em> HpTonB(30-285) with CHARMM36m force field. The last 400ns from 520ns simulation. The conformational ensemble is too collapsed here according to the comparison with experimental spin relaxation data.</p>
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 2)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains the second of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 1)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains first of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor dimer simulation - 80 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Empty micelle - 60 SDS - Na neutralized - CHARMM36m - 293K - OPC water model - replica 2 - every 100 fs
<p>Empty micelle simulation to investigate the effect of water model and peptide on SRD. Use of a higher saving frequency in order to investigate the existence of faster timescales in the relaxation data. Start frame being the end frame from "Empty micelle - 60 SDS - q0.38 - PBS neutralized - CHARMM36m - 293K - OPC water model - replica 0"</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor dimer simulation - 60 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Empty micelle - 60 SDS - Na neutralized - CHARMM36m - 293K - OPC water model - replica 0 - every 100 fs
<p>Empty micelle simulation to investigate the effect of water model and peptide on SRD. Use of a higher saving frequency in order to investigate the existence of faster timescales in the relaxation data. Start frame being the first frame from "Empty micelle - 60 SDS - q0.38 - PBS neutralized - CHARMM36m - 293K - OPC water model - replica 0"</p>
Empty micelle - 60 SDS - Na neutralized - CHARMM36m - 293K - OPC water model - replica 1 - every 100 fs
<p>Empty micelle simulation to investigate the effect of water model and peptide on SRD. Use of a higher saving frequency in order to investigate the existence of faster timescales in the relaxation data. Start frame being the middle frame from "Empty micelle - 60 SDS - q0.38 - PBS neutralized - CHARMM36m - 293K - OPC water model - replica 0"</p>
Micelle size screening - Gwalp tail anchor dimer simulation - 45 SDS - Na neutralized - CHARMM36m - 310K - OPC water model
<p>Micelle size screening by varying the amount of SDS to investigate the influence on spin relaxation data with dimers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Magaining 2 tail anchor monomer simulation - 80 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Magaining 2 tail anchor monomer simulation - 60 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Magaining 2 tail anchor monomer simulation - 120 Lipids - q0.5 - PBS neutralized - CHARMM36m - 310K - TIP3P water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide. Special iteration to investigate the influence of the water model</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor monomer simulation - 80 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor monomer simulation - 120 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor monomer simulation - 60 Lipids - q0.42 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide. Reduced saved frequency could not be generated and no-water was directly generated by hand and added here.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor monomer simulation - 60 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor monomer simulation - 120 Lipids - q0.33 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Micelle size screening - yFis1 tail anchor dimer simulation - 50SDS - Na neutralized - CHARMM36m - 310K - OPC water model
<p>Micelle size screening by varying the amount of SDS to investigate the influence on spin relaxation data with dimers of a given peptide.</p>
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