PLUMED 2: New feathers for an old bird

Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1002 Citations (Scopus)
599 Downloads (Pure)

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 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.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Original languageEnglish
Pages (from-to)604-613
Number of pages10
JournalComputer Physics Communications
Volume185
Issue number2
Early online date29 Sep 2013
DOIs
Publication statusPublished - Feb 2014

Keywords

  • Free energy
  • Molecular dynamics
  • Enhanced sampling
  • Dimensional reduction
  • MOLECULAR-DYNAMICS SIMULATIONS
  • NMR CHEMICAL-SHIFTS
  • METADYNAMICS
  • EFFICIENT
  • PROTEINS
  • PROGRAM
  • DISTRIBUTIONS
  • ALGORITHMS
  • MECHANICS
  • SOFTWARE

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