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
收藏
页码：152 / 162
页数：11
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