TIGER2: an improved algorithm for temperature intervals with global exchange of replicas.

ABSTRACT: An empirical sampling method for molecular simulation based on "temperature intervals with global exchange of replicas" (TIGER2) has been developed to reduce the high demand for computational resources and the low computational efficiency of the conventional replica-exchange molecular dynamics (REMD) method. This new method overcomes the limitation of its previous version, called TIGER, which requires the assumption of constant heat capacity during quenching of replicas from elevated temperatures to the baseline temperature. The robustness of the TIGER2 method is examined by comparing it against a Metropolis Monte Carlo simulation for sampling the conformational distribution of a single butane molecule in vacuum, a REMD simulation for sampling the behavior of alanine dipeptide in explicit

SUBMITTER: Li X 

PROVIDER: S-EPMC2719473 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature