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SSAGES : Software Suite for Advanced General Ensemble Simulations

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian 1; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; ... mehr


Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. ... mehr

Verlagsausgabe §
DOI: 10.5445/IR/1000080598
Veröffentlicht am 28.02.2018
DOI: 10.1063/1.5008853
Zitationen: 73
Web of Science
Zitationen: 72
Zitationen: 86
Cover der Publikation
Zugehörige Institution(en) am KIT Scientific Computing Center (SCC)
Universität Karlsruhe (TH) – Zentrale Einrichtungen (Zentrale Einrichtungen)
Publikationstyp Zeitschriftenaufsatz
Publikationsdatum 22.01.2018
Sprache Englisch
Identifikator ISSN: 0021-9606, 1089-7690
KITopen-ID: 1000080598
HGF-Programm 46.11.01 (POF III, LK 01) Computational Science and Mathematical Methods
Erschienen in The journal of chemical physics
Verlag American Institute of Physics (AIP)
Band 148
Heft 4
Seiten Art.Nr. 044104
Nachgewiesen in Dimensions
Web of Science
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