Faunus – a flexible framework for Monte Carlo simulation

Abstract

Faunus is a set of building blocks or ‘statistical mechanical Lego’ for constructing molecular simulation programs to study complex solutions, including proteins, polymers, salts, phospholipid membranes, surfaces and/or rigid macro-molecules. Current focus is on Metropolis Monte Carlo (MC) algorithms with support for anisotropic particles (multipolar, polarisable and sphero-cylindrical) and a flexible Hamiltonian. The design is inherently modular and it is trivial to extend functionality to cover new interaction potentials, geometries or moves. In this study, we present basic features, C++ design principles and review- selected applications. The latter includes splined pair potentials, two-dimensional parallel tempering of protein mixtures and MC swap moves for modelling ion-specific effects without ions.

Keywords::

• Metropolis Monte Carlo
• coarse graining
• C++ scientific programming

Acknowledgements

The authors are grateful for the financial support from Södra's Research Foundation; the Swedish Research Council; Organizing Molecular Matter, eSSENCE and LUNARC in Lund. RV acknowledges EU 7th Framework Program (contract No. 286154 – SYLICA) and the European Regional Development Fund (CZ.1.05/1.1.00/02.0068 CEITEC).

Notes

^1. Namely the Metropolis acceptance criterion.[6]