Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling

TitleIntegrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling
Publication TypeJournal Article
Year of Publication2014
AuthorsMori, T, Hamers, RJ, Pedersen, JA, Cui, Q
JournalJournal of Physical Chemistry B
Volume118
Pagination8210-8220
Date PublishedJul
ISBN Number1520-6106
KeywordsBINDING, BIOLOGICAL-SYSTEMS, BIOMOLECULAR SYSTEMS, FREE-ENERGY, LAMBDA-DYNAMICS, LIGAND-BINDING, LIQUID WATER, MOLECULAR-DYNAMICS SIMULATIONS, POTENTIAL FUNCTIONS, REPLICA-EXCHANGE METHOD, SINGLE SIMULATION
Abstract

Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and A-dynamics is also briefly discussed.

URL<Go to ISI>://WOS:000339368800058
Short TitleJ. Phys. Chem. B