Update 2.70 to "GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids"

被引：12

作者：

Nejahi, Younes ^{[1
]}

Barhaghi, Mohammad Soroush ^{[2
]}

Schwing, Gregory ^{[1
]}

Schwiebert, Loren ^{[1
]}

Potoff, Jeffrey ^{[2
]}

机构：

[1] Wayne State Univ, Dept Comp Sci, Detroit, MI 48202 USA

[2] Wayne State Univ, Dept Chem Engn & Mat Sci, Detroit, MI 48202 USA

来源：

SOFTWAREX | 2021年 / 13卷

基金：

美国国家科学基金会;

关键词：

Multi-particle; Exp-6; potential; Alchemical free energy; Cyclic molecules; Crankshaft move; Molecular Exchange Monte Carlo; UNITED-ATOM DESCRIPTION; TRANSFERABLE POTENTIALS; MOLECULES; IMPLEMENTATION; ALKANES; CHAIN;

D O I：

10.1016/j.softx.2020.100627

中图分类号：

TP31 [计算机软件];

学科分类号：

081202 ; 0835 ;

摘要：

Major updates in version 2.70 of GOMC include new Monte Carlo moves to enhance the sampling of phase space, such as Molecular Exchange Monte Carlo (MEMC), configurational-bias for molecules that contain rings, the crankshaft move, and a force/torque-biased multi-particle move. Support for force fields governed by exp-6 potentials, and free energy calculations using thermodynamic integration or free energy perturbation has been added. The GPU performance of the multi-particle move has been improved significantly from version 2.50, and memory usage has been reduced significantly. (C) 2020 The Author(s). Published by Elsevier B.V.

引用

页数：4

共 23 条

[1] Assessment and Optimization of Configurational-Bias Monte Carlo Particle Swap Strategies for Simulations of Water in the Gibbs Ensemble [J].

Bai, Peng ;

Siepmann, J. Ilja .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 13 (02) :431-440

[2] Effect of fluorination on the partitioning of alcohols [J].

Barhaghi, Mohammad Soroush ;

Luyet, Chloe ;

Potoff, Jeffrey J. .

MOLECULAR PHYSICS, 2019, 117 (23-24) :3827-3839

[3] Prediction of phase equilibria and Gibbs free energies of transfer using molecular exchange Monte Carlo in the Gibbs ensemble [J].

Barhaghi, Mohammad Soroush ;

Potoff, Jeffrey J. .

FLUID PHASE EQUILIBRIA, 2019, 486 :106-118

[4] Molecular exchange Monte Carlo: A generalized method for identity exchanges in grand canonical Monte Carlo simulations [J].

Barhaghi, Mohammad Soroush ;

Torabi, Korosh ;

Nejahi, Younes ;

Schwiebert, Loren ;

Potoff, Jeffrey J. .

JOURNAL OF CHEMICAL PHYSICS, 2018, 149 (07)

[5] MONTE-CARLO STUDIES ON THE FREELY JOINTED POLYMER-CHAIN WITH EXCLUDED VOLUME INTERACTION [J].

BAUMGARTNER, A ;

BINDER, K .

JOURNAL OF CHEMICAL PHYSICS, 1979, 71 (06) :2541-2545

[6]

Berendsen H.J.C., 1981, INTERMOLECULAR FORCE

[7]

Dotson D, 2017, **DATA OBJECT**, DOI [10.5281/zenodo.583647, DOI 10.5281/ZENODO.583647]

[8] ThermoData engine (TDE): Software implementation of the dynamic data evaluation concept [J].

Frenkel, M ;

Chirico, RD ;

Diky, V ;

Yan, XJ ;

Dong, Q ;

Muzny, C .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2005, 45 (04) :816-838

[9] High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD [J].

Jiang, Wei ;

Hardy, David J. ;

Phillips, James C. ;

MacKerell, Alexander D., Jr. ;

Schulten, Klaus ;

Roux, Benoit .

JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2011, 2 (02) :87-92

[10] Guidelines for the analysis of free energy calculations [J].

Klimovich, Pavel V. ;

Shirts, Michael R. ;

Mobley, David L. .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2015, 29 (05) :397-411

← 1 2 3 →