DL_MONTE: a multipurpose code for Monte Carlo simulation

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.

KEYWORDS:

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

Acknowledgements

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.

Disclosure statement

No potential conflict of interest was reported by the authors.

Notes

1 Here we use the symbols F to denote a Helmholtz free energy, G to denote a Gibbs free energy, and $\mathcal{F}$ to denote a generic free energy – either Helmholtz or Gibbs.

2 A generalisation of LSMC, named phase-switch MC, can be used to evaluate the free energy difference between a solid and a fluid. Note that in the manual, source code and training materials forDL_MONTEthe term phase-switch MC is used to refer to all such ‘switching’ MC techniques.

3 We do not count monatomic water, which was studied with LSMC in [64], as a ‘molecular system’ here since monatomic water is an ‘atomic’ force field.

Additional information

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.