Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.
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ABSTRACT:
SUBMITTER: Luchko T
PROVIDER: S-EPMC2861832 | biostudies-literature | 2010 Mar
REPOSITORIES: biostudies-literature
Publications
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.
Luchko Tyler T Gusarov Sergey S Roe Daniel R DR Simmerling Carlos C Case David A DA Tuszynski Jack J Kovalenko Andriy A
Journal of chemical theory and computation 20100301 3
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. ...[more]
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