PLUMED 2: New feathers for an old bird

2013/09/29 by Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi +2 · 3,764 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Materials Science · Physics and Astronomy · #Advanced NMR Techniques and Applications #Code (set theory) #Computer science #Field (mathematics) #Flexibility (engineering) #Implementation #Machine Learning in Materials Science #Modularity (biology) #Object-oriented programming #Programming language #Protein Structure and Dynamics #Sampling (signal processing) #Set (abstract data type) #Software #Source code #Telecommunications #Theoretical computer science #cond-mat.stat-mech #physics.bio-ph #physics.chem-ph #physics.comp-ph #q-bio.QM

paper · pdf · doi:10.1016/j.cpc.2013.09.018

published in Computer Physics Communications 185(2), 604-613 (Elsevier BV) · Accepted for publication on Computer Physics Communications

openalex publication_date 2013/09/29 · arxiv created 2013/10/03 · arxiv updated 2014/10/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

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 hardwares, 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.

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