PLUMED 2: New feathers for an old bird

PLUMED 2: New feathers for an old bird

October 4, 2013 | Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi
PLUMED 2 is an updated version of the PLUMED plug-in, designed to enhance sampling and analysis in molecular dynamics (MD) simulations. The new version is written in C++ and offers greater flexibility, modularity, and efficiency. It introduces a simplified interface with MD engines, allowing for easier integration and maintenance. PLUMED 2 can be used as a standalone program or as a library embedded in MD codes, such as GROMACS, NAMD, Quantum ESPRESSO, and LAMMPS. The software supports various collective variables (CVs) and enhanced sampling techniques, making it versatile for a wide range of applications. Key features include the ability to calculate complex CVs, perform steered MD, and implement free-energy methods like umbrella sampling, metadynamics, and steered MD. The paper also provides examples of using PLUMED 2 for steered MD, calculating functions of CVs, and analyzing the free-energy landscape of a Lennard-Jones cluster. The authors emphasize the importance of documentation and encourage users to contribute new functionalities and CVs to the community.PLUMED 2 is an updated version of the PLUMED plug-in, designed to enhance sampling and analysis in molecular dynamics (MD) simulations. The new version is written in C++ and offers greater flexibility, modularity, and efficiency. It introduces a simplified interface with MD engines, allowing for easier integration and maintenance. PLUMED 2 can be used as a standalone program or as a library embedded in MD codes, such as GROMACS, NAMD, Quantum ESPRESSO, and LAMMPS. The software supports various collective variables (CVs) and enhanced sampling techniques, making it versatile for a wide range of applications. Key features include the ability to calculate complex CVs, perform steered MD, and implement free-energy methods like umbrella sampling, metadynamics, and steered MD. The paper also provides examples of using PLUMED 2 for steered MD, calculating functions of CVs, and analyzing the free-energy landscape of a Lennard-Jones cluster. The authors emphasize the importance of documentation and encourage users to contribute new functionalities and CVs to the community.
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[slides and audio] PLUMED 2%3A New feathers for an old bird