Three-dimensional molecular theory of solvation coupled with molecular dynamics in amber

Andriy Kovalenko; Tyler Luchko; Sergey Gusarov; Daniel R. Roe; Carlos Simmerling; David A. Case; Jack Tuszynski

doi:10.1021/ct900460m

Three-dimensional molecular theory of solvation coupled with molecular dynamics in amber

Andriy Kovalenko
, Tyler Luchko
, Sergey Gusarov
, Daniel R. Roe
, Carlos Simmerling
, David A. Case
, Jack Tuszynski

Laufer Center for Physical and Quantitative Biology

National Research Council of Canada
University of Alberta
Rutgers - The State University of New Jersey, New Brunswick
National Institute of Standards and Technology

Research output: Contribution to journal › Article › peer-review

245 Scopus citations

Abstract

We present the three-dimensional molecular theory of solvation (also known as 3DRISM) 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 alaninedipeptide and protein-G.

Original language	English
Pages (from-to)	607-624
Number of pages	18
Journal	Journal of Chemical Theory and Computation
Volume	6
Issue number	3
DOIs	https://doi.org/10.1021/ct900460m
State	Published - Mar 9 2010

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10.1021/ct900460m

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title = "Three-dimensional molecular theory of solvation coupled with molecular dynamics in amber",

abstract = "We present the three-dimensional molecular theory of solvation (also known as 3DRISM) 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 alaninedipeptide and protein-G.",

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AU - Kovalenko, Andriy

AU - Luchko, Tyler

AU - Gusarov, Sergey

AU - Roe, Daniel R.

AU - Simmerling, Carlos

AU - Case, David A.

AU - Tuszynski, Jack

PY - 2010/3/9

Y1 - 2010/3/9

N2 - We present the three-dimensional molecular theory of solvation (also known as 3DRISM) 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 alaninedipeptide and protein-G.

AB - We present the three-dimensional molecular theory of solvation (also known as 3DRISM) 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 alaninedipeptide and protein-G.

UR - https://www.scopus.com/pages/publications/77950130534

U2 - 10.1021/ct900460m

DO - 10.1021/ct900460m

M3 - Article

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JO - Journal of Chemical Theory and Computation

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ER -

Three-dimensional molecular theory of solvation coupled with molecular dynamics in amber

Abstract

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