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

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...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2010-03, Vol.6 (3), p.607-624
Main Authors: Luchko, Tyler, Gusarov, Sergey, Roe, Daniel R, Simmerling, Carlos, Case, David A, Tuszynski, Jack, Kovalenko, Andriy
Format: Article
Language:English
Subjects:
AMBER
DEGREES OF FREEDOM
MATHEMATICAL METHODS AND COMPUTING
SIMULATION
SOLVATION
SOLVENTS
Statistical Mechanics
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Summary: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.
ISSN:1549-9618
1549-9626
DOI:10.1021/ct900460m