skip to main content
Idioma:

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Hopkins, Chad W ; Le Grand, Scott ; Walker, Ross C ; Roitberg, Adrian E

Journal of chemical theory and computation, 2015-04, Vol.11 (4), p.1864-1874 [Periódico revisado por pares]

United States: American Chemical Society

Texto completo disponível

Citações Citado por
  • Título:
    Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
  • Autor: Hopkins, Chad W ; Le Grand, Scott ; Walker, Ross C ; Roitberg, Adrian E
  • Assuntos: Animals ; Chickens ; Hydrogen - chemistry ; Kinetics ; Molecular Dynamics Simulation ; Muramidase - chemistry ; Muramidase - metabolism ; Principal Component Analysis ; Spin Labels ; Thermodynamics
  • É parte de: Journal of chemical theory and computation, 2015-04, Vol.11 (4), p.1864-1874
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
  • Descrição: 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 pK a 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.
  • Editor: United States: American Chemical Society
  • Idioma: Inglês
Links
Voltar para lista de resultados

  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

Buscando em bases de dados remotas. Favor aguardar.