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Dataset . 2022
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25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield

Authors: Emile de Bruyn;

25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield

Abstract

{"references": ["Tucker, M. R., Piana, S., Tan, D., LeVine, M. V., & Shaw, D. E. (2022). Development of force field parameters for the simulation of single- and double-stranded dna molecules and dna-protein complexes. The Journal of Physical Chemistry B, 126(24), 4442\u20134457. http://dx.doi.org/10.1021/acs.jpcb.1c10971", "Abraham, M. J., Murtola, T., Schulz, R., Szil\u00e1rd P\u00e1ll, Smith, J. C., Hess, B., & Lindahl, E. (2015). Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2(nil), 19\u201325. http://dx.doi.org/10.1016/j.softx.2015.06.001", "Wang, L., Friesner, R. A., & Berne, B. J. (2011). Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (rest2). The Journal of Physical Chemistry B, 115(30), 9431\u20139438. http://dx.doi.org/10.1021/jp204407d", "Alvarez, D. (2021). Juwels cluster and booster: Exascale pathfinder with modular supercomputing architecture at J\u00fclich Supercomputing Centre. Journal of large-scale research facilities JLSRF, 7, 183. http://dx.doi.org/10.17815/jlsrf-7-183"]}

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. 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. 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).

This trajectory is provided to support Jupyter Notebooks and CoLabs demonstrating the free and open-source software, SPEADI, developed by the authors.

Keywords

Alpha-Synuclein, Intrinsically Disordered Protein, Molecular Dynamics

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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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