GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

被引：149

作者：

Kobayashi, Chigusa ^{[1
]}

Jung, Jaewoon ^{[1
,2
]}

Matsunaga, Yasuhiro ^{[1
,3
]}

Mori, Takaharu ^{[2
]}

Ando, Tadashi ^{[4
,5
,6
,7
]}

Tamura, Koichi ^{[1
]}

Kamiya, Motoshi ^{[1
]}

Sugita, Yuji ^{[1
,2
,4
]}

机构：

[1] RIKEN, Computat Biophys Res Team, Adv Inst Computat Sci, Chuo Ku, 7-1-26 Minatojima Minamachi, Kobe, Hyogo 6500047, Japan

[2] RIKEN, Theoret Mol Sci Lab, 2-1 Hirosawa, Wako, Saitama 3510198, Japan

[3] JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 3320012, Japan

[4] RIKEN, Lab Biomol Funct Simulat, Quantitat Biol Ctr Computat Biol Res Core, Chuo Ku, 1-6-5 Minatojima Minamachi, Kobe, Hyogo 6500047, Japan

[5] Tokyo Univ Sci, Fac Ind Sci & Technol, Dept Appl Elect, Katsushika Ku, 6-3-1 Niijuku, Tokyo 1258585, Japan

[6] Tokyo Univ Sci, Res Inst Sci & Technol, Water Frontier Sci & Technol Res Ctr, Katsushika Ku, 6-3-1 Niijuku, Tokyo 1258585, Japan

[7] Tokyo Univ Sci, Res Inst Sci & Technol, Res Div Multiscale Interfacial Thermofluid Dynam, Katsushika Ku, 6-3-1 Niijuku, Tokyo 1258585, Japan

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2017年 / 38卷 / 25期

关键词：

molecular dynamics; string method; replica exchange molecular dynamics; graphics processing unit; multiple time step integration; BIOMOLECULAR FORCE-FIELD; PARTICLE MESH EWALD; VILLIN HEADPIECE SUBDOMAIN; FREE-ENERGY CALCULATIONS; COARSE-GRAINED MODEL; LONG-RANGE FORCES; POTENTIAL FUNCTIONS; STRING METHOD; LIQUID WATER; COLLECTIVE VARIABLES;

D O I：

10.1002/jcc.24874

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU+GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. (c) 2017 Wiley Periodicals, Inc.

引用

页码：2193 / 2206

页数：14

共 118 条

[1] GENERALIZED LANGEVIN EQUATION APPROACH FOR ATOM-SOLID-SURFACE SCATTERING - GENERAL FORMULATION FOR CLASSICAL SCATTERING OFF HARMONIC SOLIDS [J].