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

被引：221

作者：

Luchko, Tyler ^{[1
,2
,3
]}

Gusarov, Sergey ^{[1
]}

Roe, Daniel R. ^{[4
]}

Simmerling, Carlos ^{[5
,6
,7
]}

Case, David A. ^{[8
,9
]}

Tuszynski, Jack ^{[2
,10
]}

Kovalenko, Andriy ^{[1
,3
]}

机构：

[1] Natl Inst Nanotechnol, Edmonton, AB T6G 2M9, Canada

[2] Univ Alberta, Dept Phys, Edmonton, AB T6G 2G7, Canada

[3] Univ Alberta, Dept Mech Engn, Edmonton, AB T6G 2G8, Canada

[4] NIST, Gaithersburg, MD 20899 USA

[5] SUNY Stony Brook, Dept Chem, Grad Program Biochem and Struct Biol, Stony Brook, NY 11794 USA

[6] SUNY Stony Brook, Struct Biol Ctr, Stony Brook, NY 11794 USA

[7] Brookhaven Natl Lab, Computat Sci Ctr, Upton, NY 11973 USA

[8] Rutgers State Univ, BioMaPS Inst, Piscataway, NJ 08854 USA

[9] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA

[10] Univ Alberta, Dept Oncol, Edmonton, AB T6G 2G8, Canada

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2010年 / 6卷 / 03期

基金：

加拿大自然科学与工程研究理事会;

关键词：

DENSITY-FUNCTIONAL THEORY; INTEGRAL-EQUATION THEORY; INTERACTION SITE MODEL; NONUNIFORM POLYATOMIC SYSTEMS; AMBIENT AQUEOUS-SOLUTION; ALCOHOL-WATER MIXTURES; HYDRATION FREE-ENERGY; CHARGE FORCE-FIELD; ROSETTE NANOTUBES; SOLVENT MODELS;

D O I：

10.1021/ct900460m

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页码：607 / 624

页数：18

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