Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
University of Florida · Amazon (United States) · +1 more institution
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…
Citation impact
- FWCI
- 20.48
- Percentile
- 100%
- References
- 42
Authors
4Topics & keywords
- Molecular dynamics
- Chemistry
- Dihedral angle
- Lysozyme
- Discretization
- Kinetics
- Hydrogen bond
- Chemical physics