PLUMED 2: New feathers for an old bird

By Gareth A. Tribello, Massimiliano Bonomi, D. Branduardi, Carlo Camilloni, Giovanni Bussi. Computer Physics Communications, 2013

3,173 citations recorded by the source corpus.

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/b98cfb73824ae44676a61cbe321a118821512fa3

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Citations in the corpus

Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation. (2016, methodology): “2 (36) was used to include chemical-shift and distance restraints.”
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (2013, methodology): “A major help in this regard is the PLUMED package [243,244], which patches a variety of MD codes to enable users to use many of the techniques discussed here.”
Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “Variationally enhanced sampling is implemented in the VES Code module of PLUMED 2.”