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J Chem Theory Comput. 2015 Apr 14;11(4):1864-74. doi: 10.1021/ct5010406. Epub 2015 Mar 30.

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.

Author information

1
Department of Physics, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.
2
Amazon Web Services, 2201 Westlake Ave., Suite 500, Seattle, Washington 98121, United States.
3
San Diego Supercomputer Center & Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, MC0505, La Jolla, California 92093-0505, United States.
4
Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.

Abstract

Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a potentially useful tool for accelerating molecular dynamics (MD) simulations. By repartitioning the mass of heavy atoms into the bonded hydrogen atoms, it is possible to slow the highest-frequency motions of the macromolecule under study, thus allowing the time step of the simulation to be increased by up to a factor of 2. In this communication, we investigate further how this mass repartitioning allows the simulation time step to be increased in a stable fashion without significantly increasing discretization error. To this end, we ran a set of simulations with different time steps and mass distributions on a three-residue peptide to get a comprehensive view of the effect of mass repartitioning and time step increase on a system whose accessible phase space is fully explored in a relatively short amount of time. We next studied a 129-residue protein, hen egg white lysozyme (HEWL), to verify that the observed behavior extends to a larger, more-realistic, system. Results for the protein include structural comparisons from MD trajectories, as well as comparisons of pKa calculations via constant-pH MD. We also calculated a potential of mean force (PMF) of a dihedral rotation for the MTS [(1-oxyl-2,2,5,5-tetramethyl-pyrroline-3-methyl)methanethiosulfonate] spin label via umbrella sampling with a set of regular MD trajectories, as well as a set of mass-repartitioned trajectories with a time step of 4 fs. Since no significant difference in kinetics or thermodynamics is observed by the use of fast HMR trajectories, further evidence is provided that long-time-step HMR MD simulations are a viable tool for accelerating MD simulations for molecules of biochemical interest.

PMID:
26574392
DOI:
10.1021/ct5010406
[Indexed for MEDLINE]

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