Lattice-switching Monte Carlo method for crystals of flexible molecules

Bridgwater, Sally; Quigley, David

doi:10.1103/physreve.90.063313

Cited by 6 publications

(16 citation statements)

References 30 publications

(44 reference statements)

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“…In 'atomic' systems, where the particles have no internal degrees of freedom (e.g., orientation, bond angles and lengths), the description of the switch transformation given above is sufficient. However, for molecular systems there is the question of how to transform the particles' internal degrees of freedom during the switch [67]. In this work we only consider molecular systems comprised of rigid molecules, for which the orientations of the molecules constitute the internal degrees of freedom.…”

Section: Methodsmentioning

confidence: 99%

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DL_MONTE: a multipurpose code for Monte Carlo simulation

Brukhno

Grant

Underwood

et al. 2019

Molecular Simulation

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DL MONTE is an open source, general-purpose software package for performing Monte Carlo 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, focusing 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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Section: Methodsmentioning

confidence: 99%

“…However, while there have been many applications of LSMC to atomic systems (including 'atomic' soft-matter such as hard spheres), applications to molecular systems have been few 3 . The only studies we are aware of are [65] (where LSMC was applied to colloidal hard dumbbells), [66] (calcium carbonate) and [67] (butane).…”

Section: Lattice-switch Monte Carlomentioning

confidence: 99%

DL_MONTE: a multipurpose code for Monte Carlo simulation

Brukhno

Grant

Underwood

et al. 2019

Molecular Simulation

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“…8 With this p 2 can be obtained from the above equation (M = 1 in Eqn. (13)). This in turn can be used to obtain p 3 (M = 2 in Eqn.…”

Section: Transition Matrix Methodsmentioning

confidence: 99%

“…This in turn can be used to obtain p 3 (M = 2 in Eqn. (13)), which in turn can be used to obtain p 4 , etc., until p N macro is obtained. Finally, one normalises the resulting function p M such that…”

Section: Transition Matrix Methodsmentioning

confidence: 99%

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monteswitch : A package for evaluating solid–solid free energy differences via lattice-switch Monte Carlo

Underwood

Ackland

2017

Computer Physics Communications

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Lattice-switch Monte Carlo (LSMC) is a method for evaluating the free energy between two given solid phases. LSMC is a general method, being applicable to a wide range of problems and interatomic potentials. Furthermore it is extremely efficient, ostensibly more efficient than other existing general methods. Here we introduce a package, monteswitch, which can be used to perform LSMC simulations. The package can be used to evaluate the free energy differences between pairs of solid phases, including multicomponent phases, via LSMC for atomic (i.e., non-molecular) systems in the NVT and NPT ensembles. It could also be used to evaluate the free energy cost associated with interfaces and defects. Regarding interatomic potentials, monteswitch currently supports various commonly-used pair potentials, including the hard-sphere, Lennard-Jones, and Morse potentials, as well as the embedded atom model. However the main strength of the package is its versatility: it is designed so that users can easily implement their own potentials. the free energy difference between two solid phases. The package presented here allows LSMC simulations to be performed for a variety of interatomic potentials, including commonly-used pair potentials and the embedded atom model. Furthermore the package is designed so that users can easily implement their own potentials. The package supports LSMC simulations in the NVT and NPT ensembles, and can treat multicomponent systems. A version of the main program is included which is parallelised using MPI. This program parallelises the LSMC calculation by simulating multiple replicas of the system in parallel. KeywordsRestrictions: monteswitch cannot treat molecular systems, i.e., systems in which the particles exhibit rotational degrees of freedom, and is restricted to systems which can be represented within an orthorhombic supercell. Furthermore, the interatomic potential is 'hard-coded' in the sense that implementing a different potential requires that the package be recompiled. Additional comments: monteswitch includes programs to assist with the creation of input files and the post-processing of output files created by the main Monte Carlo programs. A user manual, a suite of test cases, a worked example, and a collection of plug-ins to implement various commonly-used interatomic potentials are also included with the package. Running time: Depends on the nature of the problem and the underlying computing platform. For the Zr EAM example in the manuscript one iteration (i.e., one 160,000-sweep weight-function-generation simulation and one 700,000-sweep production simulation) took a wall-clock time of approximately 1.9 hours on a desktop machine (an iMac14,2 with a 3.2GHz Intel Core i5-4570 processor) exploiting 4 cores for the 384-atom system, and 17.7 hours for the 1296-atom system. For each ensemble in the hard-sphere example the 18,000,000-sweep weight-function-generation simulation and two 125,000,000-sweep production simulations took a total of approximately 11 hours exploiting 16 core...

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Evaluation of General and Tailor Made Force Fields via X-ray Thermal Diffuse Scattering Using Molecular Dynamics and Monte Carlo Simulations of Crystalline Aspirin

Chan

Neumann²

2018

J. Chem. Theory Comput.

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We have performed a comparison of the experimental thermal diffuse scattering (TDS) from crystalline Aspirin (form I) to that calculated from molecular dynamics (MD) simulations based on a variety of general force fields and a tailor-made force field (TMFF). A comparison is also made with Monte Carlo (MC) simulations which use a "harmonic network" approach to describe the intermolecular interactions. These comparisons were based on the hypothesis that TDS could be a useful experimental data in validation of such simulation parameter sets, especially when calculations of dynamical properties (e.g., thermodynamic free energies) from molecular crystals are concerned. Currently such a validation of force field parameters against experimental data is often limited to calculation of specific physical properties, e.g., absolute lattice energies usually at 0 K or heat capacity measurements. TDS harvested from in-house or synchrotron experiments comprises highly detailed structural information representative of the dynamical motions of the crystal lattice. Thus, TDS is a well-suited experimental data-driven means of cross validating theoretical approaches targeted at understanding dynamical properties of crystals. We found from the results of our investigation that the TMFF and COMPASS (from the commercial software "Materials Studio") parameter sets gave the best agreement with experiment. From our homologous MC simulation analysis we are able to show that force constants associated with the molecular torsion angles are likely to be a strong contributing factor for the apparent reason why these aforementioned force fields performed better.

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Lattice-switching Monte Carlo method for crystals of flexible molecules

Cited by 6 publications

References 30 publications

DL_MONTE: a multipurpose code for Monte Carlo simulation

DL_MONTE: a multipurpose code for Monte Carlo simulation

monteswitch : A package for evaluating solid–solid free energy differences via lattice-switch Monte Carlo

Evaluation of General and Tailor Made Force Fields via X-ray Thermal Diffuse Scattering Using Molecular Dynamics and Monte Carlo Simulations of Crystalline Aspirin

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