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Simulated Solute Tempering
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DOI：10.1021/ct900274n.png)
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Abstract
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For the enhanced conformational sampling in molecular dynamics (MD) simulations, we present simulated solute tempering (SST) which is an easy to implement variant of simulated tempering. SST extends conventional simulated tempering (CST) by key concepts of replica exchange with solute tempering (REST, Liu et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749). We have applied SST, CST, and REST to molecular dynamics (MD) simulations of an alanine octapeptide in explicit water. The weight parameters required for CST and SST are determined by two different formulas whose performance is compared. For SST only one of them yields a uniform sampling of the temperature space. Compared to CST and REST, SST provides the highest exchange probabilities between neighboring rungs in the temperature ladder. Concomitantly, SST leads to the fastest diffusion of the simulation system through the temperature space, in particular, if the even-odd exchange scheme is employed in SST. As a result, SST exhibits the highest sampling speed of the investigated tempering methods.
Keywords:
MOLECULAR-DYNAMICS SIMULATIONS
FREE-ENERGY CALCULATIONS
GENERALIZED-ENSEMBLE ALGORITHMS
REPLICA-EXCHANGE SIMULATIONS
BETA-HAIRPIN
MONTE-CARLO
EXPLICIT WATER
ELECTROSTATIC INTERACTIONS
MULTIPOLE METHOD
PEPTIDE
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