Please use this identifier to cite or link to this item: http://hdl.handle.net/1959.3/190477

Title

A scalable parallel Monte Carlo method for free energy simulations of molecular systems

Author(s)

Khan, Malek O.;  Kennedy, Gareth;  Chan, Derek Y. C.

Abstract

We present a method of parallelizing flat histogram Monte Carlo simulations, which give the free energy of a molecular system as an output. In the serial version, a constant probability distribution, as a function of any system parameter, is calculated by updating an external potential that is added to the system Hamiltonian. This external potential is related to the free energy. In the parallel implementation, the simulation is distributed on to different processors. With regular intervals the modifying potential is summed over all processors and distributed back to every processor, thus spreading the information of which parts of parameter space have been explored. This implementation is shown to decrease the execution time linearly with added number of processors.

Publication type

Journal article

Source

Journal of Computational Chemistry, Vol. 26, no. 1 (Jan 2005), pp. 72-77

Publication year

2005

FOR Code(s)

0306 Physical Chemistry (Incl. Structural);  0307 Theoretical and Computational Chemistry

Keyword(s)

Chemical model;  Computer simulation;  Energy transfer;  Free energy;  Hamiltonians;  High performance computing;  Large systems;  Molecular simulations;  Monte Carlo methods;  Parallel computing;  Parallel processing systems;  Probability distributions;  Problem solving;  Supercomputers;  System parameters;  Thermodynamics

Publisher

John Wiley & Sons

ISSN

0192-8651

Publisher URL

http://dx.doi.org/10.1002/jcc.20143

Copyright

Copyright © 2004 Wiley Periodicals, Inc.

Peer reviewed