Journal Article

FZJ-2020-04933

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png CORE-MD, a path correlated molecular dynamics simulation method

Peter, E. K.FZJ* ; Shea, J.-E. ; Schug, A. (Corresponding author)FZJ*

2020
American Institute of Physics Melville, NY

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Please use a persistent id in citations: http://hdl.handle.net/2128/26555  doi:10.1063/5.0015398

Abstract: We present an enhanced Molecular Dynamics (MD) simulation method, which is free from the requirement of a priori structural information of the system. The technique is capable of folding proteins with very low computational effort and requires only an energy parameter. The path correlated MD (CORE-MD) method uses the autocorrelation of the path integral over the reduced action and propagates the system along the history dependent path correlation. We validate the new technique in simulations of the conformational landscapes of dialanine and the TrpCage mini-peptide. We find that the novel method accelerates the sampling by three orders of magnitude and observe convergence of the conformational sampling in both cases. We conclude that the new method is broadly applicable for the enhanced sampling in MD simulations. The CORE-MD algorithm reaches a high accuracy compared with long time equilibrium MD simulations.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. John von Neumann - Institut für Computing (NIC)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. Forschergruppe Schug (hkf6_20200501) (hkf6_20200501)

Appears in the scientific report 2020

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Database coverage:
; ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; Ebsco Academic Search ; Essential Science Indicators ; IF < 5 ; JCR ; National-Konsortium ; Nationallizenz ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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