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Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Journal article   Open access  Peer reviewed

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

Tyler Luchko, Sergey Gusarov, Daniel R Roe, Carlos Simmerling, David A Case, Jack Tuszynski, Andriy Kovalenko and BROOKHAVEN NATIONAL LABORATORY (BNL)
Journal of chemical theory and computation, Vol.6(3), pp.607-624
03/01/2010
PMCID: PMC2861832
PMID: 20440377

Abstract

Chemistry Chemistry, Physical Physical Sciences Physics Physics, Atomic, Molecular & Chemical Science & Technology
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 multiple 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.
url
https://doi.org/10.1021/ct900460mView
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