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4 results for “REST2”
Replica-Exchange with Solute Tempering (REST2) Simulations of Histone Tails
<p>Replica at 300 K 1 bar 1 µs trajectories and corresponding parameter files for histone tails alone or with a DNA fragment. The parameter files containing IDP modification are indicated as "idp". </p><p>With DNA fragment, the trajectories are given without solvent and ion and called "nosol". </p>
100ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the DES-Amber Forcefield
<p>Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the DES-Amber force field published by Maxwell et al. The simulation was run for 100 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K.</p> <p>This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers.</p> <p>The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).</p>
25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield
<p>Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the a99SB-disp force field published by Maxwell et al. The simulation was run for 25 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K.</p> <p>This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers.</p> <p>The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).</p>
ELF3 prion-like domain REST2 simulation trajectories
<p>This dataset contains ELF3 prion-like domain (PrD) trajectories obtained with replica exchange with solute tempering (REST2). These trajectories were created as part of a publication exploring the temperature-responsive condensation of the ELF3-PrD in the scientific pulication titled, "Molecular dynamics simulations illuminate the role of sequence context in the ELF3-PrD-based temperature sensing mechanism in plants." Included are trajectories for ELF3-PrD variants including wildtype, 0Q (variable poly-glutamine tract removed), and an F527A mutant, each at a range of temperatures between 290K and 405K.</p>
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