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

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

30 Apr 2009 | Massimiliano Bonomi, Davide Branduardi, Giovanni Bussi, Carlo Camilloni, Davide Provasi, Paolo Raiteri, Davide Donadio, Fabrizio Marinelli, Fabio Pietrucci, Ricardo A. Broglia, Michele Parrinello
PLUMED is a plugin for free-energy calculations in molecular dynamics simulations. It allows users to interface with popular MD codes such as GROMACS, NAMD, DLPOLY, and SANDER through a simple patching procedure. The plugin supports various enhanced sampling techniques, including metadynamics, umbrella sampling, and Jarzynski-equation based steered MD. It is written in ANSI-C and can be easily integrated with fortran and C/C++ codes. PLUMED provides a wide range of collective variables (CVs) for free-energy calculations, enabling the study of complex biological and condensed matter systems. The software is available under the Lesser GPL license and can be downloaded from http://merlino.mi.infn.it/plumed. It is designed to be portable and compatible with multiple MD engines, allowing users to choose the most suitable code based on their simulation needs. The plugin includes a variety of tools and test cases to facilitate free-energy calculations. PLUMED has been tested on various systems, including the alanine dipeptide, demonstrating its effectiveness in calculating free-energy landscapes. The software is expected to be further expanded in the future to support more MD codes and methods.PLUMED is a plugin for free-energy calculations in molecular dynamics simulations. It allows users to interface with popular MD codes such as GROMACS, NAMD, DLPOLY, and SANDER through a simple patching procedure. The plugin supports various enhanced sampling techniques, including metadynamics, umbrella sampling, and Jarzynski-equation based steered MD. It is written in ANSI-C and can be easily integrated with fortran and C/C++ codes. PLUMED provides a wide range of collective variables (CVs) for free-energy calculations, enabling the study of complex biological and condensed matter systems. The software is available under the Lesser GPL license and can be downloaded from http://merlino.mi.infn.it/plumed. It is designed to be portable and compatible with multiple MD engines, allowing users to choose the most suitable code based on their simulation needs. The plugin includes a variety of tools and test cases to facilitate free-energy calculations. PLUMED has been tested on various systems, including the alanine dipeptide, demonstrating its effectiveness in calculating free-energy landscapes. The software is expected to be further expanded in the future to support more MD codes and methods.
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