Implementation of replica-exchange umbrella sampling in GAMESS

被引：9

作者：

Ito, Shingo ^{[1
]}

Fedorov, Dmitri G. ^{[2
]}

Okamoto, Yuko ^{[3
,4
,5
,6
,7
]}

Irle, Stephan ^{[1
,8
,9
]}

机构：

[1] Nagoya Univ, Grad Sch Sci, Dept Chem, Nagoya, Aichi 4648602, Japan

[2] Natl Inst Adv Ind Sci & Technol, Res Ctr Computat Design Adv Funct Mat CD FMat, Tsukuba, Ibaraki 3058568, Japan

[3] Nagoya Univ, Grad Sch Sci, Dept Phys, Nagoya, Aichi 4648602, Japan

[4] Nagoya Univ, Struct Biol Res Ctr, Grad Sch Sci, Nagoya, Aichi 4648602, Japan

[5] Nagoya Univ, Ctr Computat Sci, Grad Sch Engn, Nagoya, Aichi 4648603, Japan

[6] Nagoya Univ, Informat Technol Ctr, Nagoya, Aichi 4648601, Japan

[7] CREST, JST, Nagoya, Aichi 4648602, Japan

[8] Nagoya Univ, WPI, Inst Transformat Biomol, Nagoya, Aichi 4648601, Japan

[9] Oak Ridge Natl Lab, Computat Sci & Engn Div, POB 2009, Oak Ridge, TN 37831 USA

来源：

COMPUTER PHYSICS COMMUNICATIONS | 2018年 / 228卷

关键词：

Replica-exchange molecular dynamics; Multidimensional replica-exchange method; Umbrella sampling; Replica-exchange umbrella sampling; Density-functional tight-binding; GAMESS-US; GENERALIZED-ENSEMBLE ALGORITHMS; MOLECULAR-ORBITAL METHOD; MONTE-CARLO METHOD; FREE-ENERGY; DYNAMICS; SIMULATIONS; INTERFACE; EFFICIENT; MODELS;

D O I：

10.1016/j.cpc.2018.01.014

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation. (C) 2018 Published by Elsevier B.V.

引用

页码：152 / 162

页数：11

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