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Replica exchange with solute tempering: efficiency in large scale systems.

ABSTRACT: We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an alpha-helix, a beta-hairpin, and a TrpCage, with these peptides defined as the "central group". We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein-ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper.

SUBMITTER: Huang X

PROVIDER: S-EPMC2744475 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature

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Replica exchange with solute tempering: efficiency in large scale systems.

Huang Xuhui X Hagen Morten M Kim Byungchan B Friesner Richard A RA Zhou Ruhong R Berne B J BJ

The journal of physical chemistry. B 20070417 19

We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an alpha-helix, a beta-hairpin, and a TrpCage, with these peptides defined as the "central group". We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappea ...[more]

PMID: 17439169

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