A scalable parallel Monte Carlo method for free energy simulations of molecular systems.
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.
Khan
Malek O
MO
Particulate Fluids Processing Centre, Department of Mathematics & Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia.
Kennedy
Gareth
G
Chan
Derek Y C
DY
D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D009010:Monte Carlo Method; D013816:Thermodynamics