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

✍ Scribed by Malek O. Khan; Gareth Kennedy; Derek Y. C. Chan

Publisher
John Wiley and Sons
Year
2004
Tongue
English
Weight
234 KB
Volume
26
Category
Article
ISSN
0192-8651

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✦ Synopsis

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. Β© 2004 Wiley Periodicals, Inc. J Comput Chem 26: 72–77, 2005

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