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