PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Details PLUMED: a portable plugin for free-energy calculations with molecular dynamics PLUMED: a portable plugin for free-energy calculations with molecular dynamics

2009-02-05

arxiv.org/abs/0902.0874v3

Bonomi et al, Comp. Phys. Comm. 180, 1961 (2009)

Physics

Computational Physics

to be submitted to Computer Physics Communications

Scientific paper

10.1016/j.cpc.2009.05.011

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.

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