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Abstract
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.
Original language | English |
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Pages (from-to) | 131-151 |
Number of pages | 21 |
Journal | Molecular Simulation |
Volume | 47 |
Issue number | 2-3 |
Early online date | 1 Feb 2019 |
DOIs | |
Publication status | Published - 31 Dec 2021 |
Funding
This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) under Grant EP/M011291/1. Kevin Stratford was funded under the embedded CSE programme of the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk): project eCSE04-4. This work made use of the Balena High Performance Computing Service at the University of Bath. Computing resources were also provided by STFC Scientific Computing Department's SCARF HPC cluster [75]. The support of CCP5 [36] is gratefully acknowledged, as are valuable discussions with Graeme Ackland.
Funders | Funder number |
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Engineering and Physical Sciences Research Council | EP/M011291/1 |
Science and Technology Facilities Council | |
University of Bath |
Keywords
- free energy
- molecular modelling
- Monte Carlo
- MPI
- open-source software
ASJC Scopus subject areas
- General Chemistry
- Information Systems
- Modelling and Simulation
- General Chemical Engineering
- General Materials Science
- Condensed Matter Physics
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- 1 Finished
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DL-MONTE Monte Carlo Simulation of Condensed Phases
Wilding, N. (PI) & Parker, S. (CoI)
Engineering and Physical Sciences Research Council
31/03/15 → 30/03/18
Project: Research council