Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
- 1 February 2010
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of Chemical Theory and Computation
- Vol. 6 (3), 607-624
- https://doi.org/10.1021/ct900460m
Abstract
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.Keywords
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