Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes. Program summary: Program title: PLUMED. Catalogue identifier: AEEE_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Lesser GPL. No. of lines in distributed program, including test data, etc.: 107 505. No. of bytes in distributed program, including test data, etc.: 2 052 759. Distribution format: tar.gz. Programming language: ANSI-C. Computer: Any computer capable of running an executable produced by GCC compiler. Operating system: Linux/Unix. RAM: Depending on the number of atoms, the method chosen and the collective variables used. Classification: 23. External routines: Must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER). Nature of problem: Calculation of free-energy surfaces for biological and condensed matter systems. Solution method: Implementation of various enhanced sampling techniques. Unusual features: PLUMED is not a stand-alone program but it must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER) that needs to be recompiled. Each interface is provided in a patch form. Running time: Depending on the number of atoms, the method chosen and the collective variables used. © 2009 Elsevier B.V. All rights reserved.

PLUMED: A portable plugin for free-energy calculations with molecular dynamics / M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia, M. Parrinello. - In: COMPUTER PHYSICS COMMUNICATIONS. - ISSN 0010-4655. - 180:10(2009), pp. 1961-1972. [10.1016/j.cpc.2009.05.011]

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

C. Camilloni;D. Provasi;R.A. Broglia
Penultimo
;
2009

Abstract

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes. Program summary: Program title: PLUMED. Catalogue identifier: AEEE_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Lesser GPL. No. of lines in distributed program, including test data, etc.: 107 505. No. of bytes in distributed program, including test data, etc.: 2 052 759. Distribution format: tar.gz. Programming language: ANSI-C. Computer: Any computer capable of running an executable produced by GCC compiler. Operating system: Linux/Unix. RAM: Depending on the number of atoms, the method chosen and the collective variables used. Classification: 23. External routines: Must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER). Nature of problem: Calculation of free-energy surfaces for biological and condensed matter systems. Solution method: Implementation of various enhanced sampling techniques. Unusual features: PLUMED is not a stand-alone program but it must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER) that needs to be recompiled. Each interface is provided in a patch form. Running time: Depending on the number of atoms, the method chosen and the collective variables used. © 2009 Elsevier B.V. All rights reserved.
Free energy; Metadynamics; Molecular dynamics; Proteins; Umbrella sampling; Hardware and Architecture; Physics and Astronomy (all)
Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/494867
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