CORE-MD, a path correlated molecular dynamics simulation method

Emanuel K Peter; Joan-Emma Shea; Alexander Schug

doi:10.1063/5.0015398

CORE-MD, a path correlated molecular dynamics simulation method

J Chem Phys. 2020 Aug 28;153(8):084114. doi: 10.1063/5.0015398.

Authors

Emanuel K Peter¹, Joan-Emma Shea², Alexander Schug¹

Affiliations

¹ John von Neumann Institute for Computing and Julich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany.
² Department of Chemistry and Biochemistry, Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA.

PMID: 32872878
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.

MeSH terms

Algorithms
Dipeptides / chemistry*
Models, Chemical*
Models, Molecular
Molecular Dynamics Simulation*
Peptides / chemistry*
Protein Conformation
Protein Folding

Substances

Dipeptides
Peptides
alanylalanine