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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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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cited_by cdi_FETCH-LOGICAL-a432t-3d51533afbf0e272e4e487f7a82c3cc745af23b7cebf383d50e253ee8fc4d4a53
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container_issue 3
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container_title Journal of chemical theory and computation
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creator Luchko, Tyler
Gusarov, Sergey
Roe, Daniel R
Simmerling, Carlos
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Tuszynski, Jack
Kovalenko, Andriy
description 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.
doi_str_mv 10.1021/ct900460m
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source American Chemical Society:Jisc Collections:American Chemical Society Read & Publish Agreement 2022-2024 (Reading list)
subjects AMBER
DEGREES OF FREEDOM
MATHEMATICAL METHODS AND COMPUTING
SIMULATION
SOLVATION
SOLVENTS
Statistical Mechanics
title Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
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