swMATH ID: 2631
Software Authors: Akhmatskaya, Elena; Reich, Sebastian
Description: GSHMC: An efficient method for molecular simulation. The hybrid Monte Carlo (HMC) method is a popular and rigorous method for sampling from a canonical ensemble. The HMC method is based on classical molecular dynamics simulations combined with a Metropolis acceptance criterion and a momentum resampling step. While the HMC method completely resamples the momentum after each Monte Carlo step, the generalized hybrid Monte Carlo (GHMC) method can be implemented with a partial momentum refreshment step. This property seems desirable for keeping some of the dynamic information throughout the sampling process similar to stochastic Langevin and Brownian dynamics simulations. It is, however, ultimate to the success of the GHMC method that the rejection rate in the molecular dynamics part is kept at a minimum. Otherwise an undesirable Zitterbewegung in the Monte Carlo samples is observed. In this paper, we describe a method to achieve very low rejection rates by using a modified energy, which is preserved to high-order along molecular dynamics trajectories. The modified energy is based on backward error results for symplectic time-stepping methods. The proposed generalized shadow hybrid Monte Carlo (GSHMC) method is applicable to NVT as well as NPT ensemble simulations.
Homepage: http://www.sciencedirect.com/science/article/pii/S0021999108000533
Related Software: Gromacs; NUTS; PyMC; Stan; CODA; UCI-ml; BUGS; PRMLT; MCMCglmm; Mcmcpack; WinBUGS; RODAS; EnKF; ProtoMol; SQPlab; LINCS
Cited in: 16 Documents

Standard Articles

1 Publication describing the Software, including 1 Publication in zbMATH Year
GSHMC: An efficient method for molecular simulation. Zbl 1148.82316
Akhmatskaya, Elena; Reich, Sebastian

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