TY - JOUR
T1 - Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
AU - Grønbech-Jensen, Niels
AU - Hayre, Natha Robert
AU - Farago, Oded
N1 - Funding Information:
The authors thank George Batrouni, Daniel Cox, Richard Scalettar, and Rajiv Singh for encouraging discussions. This work was supported primarily by the US Department of Energy Project DE-NE0000536000. The work was also supported by the Research Investments in the Sciences and Engineering (RISE) Program (UC Davis) and US NSF Grant DMR-1207624 .
PY - 2014/2/1
Y1 - 2014/2/1
N2 - A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Störmer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity.
AB - A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Störmer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity.
KW - Molecular dynamics
KW - Simulated Langevin dynamics
KW - Stochastic differential equations
KW - Verlet algorithm
UR - http://www.scopus.com/inward/record.url?scp=84888642157&partnerID=8YFLogxK
U2 - 10.1016/j.cpc.2013.10.006
DO - 10.1016/j.cpc.2013.10.006
M3 - Article
AN - SCOPUS:84888642157
SN - 0010-4655
VL - 185
SP - 524
EP - 527
JO - Computer Physics Communications
JF - Computer Physics Communications
IS - 2
ER -