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Fakultät für Physik


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Impressum
(c) 2002 BMO

"Simulated solute tempering"
Robert Denschlag, Martin Lingenheil, Paul Tavan, Gerald Mathias
J. Chem. Theory Comput. 5, 28474-2857 (2009)


Abstract:
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. (2005) Proc. Natl. Acad. Sci. USA 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.

BMO authors (in alphabetic order):
Robert Denschlag
Martin Lingenheil
Gerald Mathias
Paul Tavan

Assoziierte Projekte:
Structural Stability of the Cellular Prion Protein PrPC studied by MD-Simulations
Photoswitchable model peptides and their conformational dynamics


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Letzte Änderung: 2016-09-14 13:34