Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Journal of Chemical Theory and Computation2010Vol. 6(3), pp. 607–624
Citations Over TimeTop 10% of 2010 papers
Tyler Luchko, Sergey Gusarov, Daniel R. Roe, Carlos Simmerling, David A. Case, Jack A. Tuszyński, Andriy Kovalenko
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 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.
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