PLUMED 2: New feathers for an old bird

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

doi:10.1016/j.cpc.2013.09.018

PLUMED 2: New feathers for an old bird

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

^*Corresponding author for this work

School of Mathematics and Physics

Research output: Contribution to journal › Article › peer-review

2332 Citations (Scopus)

1808 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.

Original language	English
Pages (from-to)	604-613
Number of pages	10
Journal	Computer Physics Communications
Volume	185
Issue number	2
Early online date	29 Sept 2013
DOIs	https://doi.org/10.1016/j.cpc.2013.09.018
Publication status	Published - 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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10.1016/j.cpc.2013.09.018

PLUMED 2: New feathers for an old bird
Copyright 2013 Elsevier B.V. All rights reserved. This is a pre-print of a work finally published at http://dx.doi.org/10.1016/j.cpc.2013.09.018
Submitted manuscript, 1.03 MB

Gareth Tribello
- g.tribelloqub.acuk
Person: Academic

Cite this

@article{fb4797d2871c4d68b2a410d02d59d55a,

title = "PLUMED 2: New feathers for an old bird",

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 summaryProgram title: PLUMED 2Catalogue identifier: AEEE_v2_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: YesNo. of lines in distributed program, including test data, etc.: 700646No. of bytes in distributed program, including test data, etc.: 6618136Distribution format: tar.gzProgramming 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.",

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

author = "Tribello, {Gareth A.} and Massimiliano Bonomi and Davide Branduardi and Carlo Camilloni and Giovanni Bussi",

year = "2014",

month = feb,

doi = "10.1016/j.cpc.2013.09.018",

language = "English",

volume = "185",

pages = "604--613",

journal = "Computer Physics Communications",

issn = "0010-4655",

publisher = "Elsevier B.V.",

number = "2",

}

TY - JOUR

T1 - PLUMED 2: New feathers for an old bird

AU - Tribello, Gareth A.

AU - Bonomi, Massimiliano

AU - Branduardi, Davide

AU - Camilloni, Carlo

AU - Bussi, Giovanni

PY - 2014/2

Y1 - 2014/2

N2 - 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 summaryProgram title: PLUMED 2Catalogue identifier: AEEE_v2_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: YesNo. of lines in distributed program, including test data, etc.: 700646No. of bytes in distributed program, including test data, etc.: 6618136Distribution format: tar.gzProgramming 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.

AB - 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 summaryProgram title: PLUMED 2Catalogue identifier: AEEE_v2_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: YesNo. of lines in distributed program, including test data, etc.: 700646No. of bytes in distributed program, including test data, etc.: 6618136Distribution format: tar.gzProgramming 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.

KW - Free energy

KW - Molecular dynamics

KW - Enhanced sampling

KW - Dimensional reduction

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - NMR CHEMICAL-SHIFTS

KW - METADYNAMICS

KW - EFFICIENT

KW - PROTEINS

KW - PROGRAM

KW - DISTRIBUTIONS

KW - ALGORITHMS

KW - MECHANICS

KW - SOFTWARE

U2 - 10.1016/j.cpc.2013.09.018

DO - 10.1016/j.cpc.2013.09.018

M3 - Article

SN - 0010-4655

VL - 185

SP - 604

EP - 613

JO - Computer Physics Communications

JF - Computer Physics Communications

IS - 2

ER -

PLUMED 2: New feathers for an old bird

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