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CORE-MD, a path correlated molecular dynamics simulation method
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DOI：10.1063/5.0015398.png)
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Abstract
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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.
Keywords:
FREE-ENERGY LANDSCAPE
TRP-CAGE PROTEIN
FOLDING PROTEINS
ALANINE DIPEPTIDE
ALGORITHM
KINETICS
SHAKE
SPECTROSCOPY
STABILITY
ENTROPY
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