4.3 Article

DL_MONTE: a multipurpose code for Monte Carlo simulation

期刊

MOLECULAR SIMULATION
卷 47, 期 2-3, 页码 131-151

出版社

TAYLOR & FRANCIS LTD
DOI: 10.1080/08927022.2019.1569760

关键词

Monte Carlo; free energy; molecular modelling; open-source software; MPI

资金

  1. EPSRC [EP/M011291/1] Funding Source: UKRI

向作者/读者索取更多资源

DL_MONTE is an open-source software package for Monte Carlo simulations, with a wide range of force fields and techniques applicable to molecular simulation. Recent key features added include handling systems confined to planar pores, lattice-switch Monte Carlo method for precise free energy differences, and various methods for evaluating free energy profiles.
DL_MONTE is an open-source, general-purpose software package for performing Monte Carlo (MC) simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation. Here we provide an overview of DL_MONTE, focussing on key features recently added to the package. These include the ability to treat systems confined to a planar pore (i.e. 'slit' or 'slab' boundary conditions); the lattice-switch Monte Carlo (LSMC) method for evaluating precise free energy differences between competing polymorphs; various commonly used methods for evaluating free energy profiles along transition pathways (including umbrella sampling, Wang-Landau and transition matrix); and a supplementary Python toolkit for simulation management and application of the histogram reweighting analysis method. We provide two 'real-world' examples to elucidate the use of these methods in DL_MONTE. In particular, we apply umbrella sampling to calculate the free energy profile associated with the translocation of a lipid through a bilayer. Moreover, we employ LSMC to examine the thermodynamic stability of two plastic crystal phases of water at high pressure. Beyond this, we provide instructions on how to access DL_MONTE and point to additional information valuable to existing and prospective users.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.3
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据