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dc.contributor.authorBonomi, M.
dc.contributor.authorBranduardi, D.
dc.contributor.authorBussi, G.
dc.contributor.authorCamilloni, C.
dc.contributor.authorProvasi, D.
dc.contributor.authorRaiteri, Paolo
dc.contributor.authorDonadio, D.
dc.contributor.authorMarinelli, F.
dc.contributor.authorPietrucci, F.
dc.contributor.authorBroglia, R.
dc.contributor.authorParrinello, M.
dc.date.accessioned2017-01-30T13:51:31Z
dc.date.available2017-01-30T13:51:31Z
dc.date.created2009-09-08T20:01:55Z
dc.date.issued2009
dc.identifier.citationBonomi, Massimiliano and Branduardi, Davide and Bussi, Giovanni and Camilloni, Carlo and Provasi, Davide and Raiteri, Paolo and Donadio, Davide and Marinelli, Fabrizio and Pietrucci, Fabio and Broglia, Ricardo and Parrinello, Michele. 2009. PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications. 180 (10): pp. 1961-1972.
dc.identifier.urihttp://hdl.handle.net/20.500.11937/35745
dc.identifier.doi10.1016/j.cpc.2009.05.011
dc.description.abstract

Here we present a program aimed at free-energy calculations in molecular systems. It consists of aseries 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. Freeenergy 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.

dc.publisherElsevier
dc.titlePLUMED: a portable plugin for free-energy calculations with molecular dynamics
dc.typeJournal Article
dcterms.source.volume180
dcterms.source.number10
dcterms.source.startPage1961
dcterms.source.endPage1972
dcterms.source.issn00104655
dcterms.source.titleComputer Physics Communications
curtin.note

The link to the journal's home page is: http://www.elsevier.com/wps/find/journaldescription.cws_home/505710/description#description

curtin.note

Copyright © 2009 Elsevier B.V. All rights reserved.

curtin.accessStatusOpen access
curtin.facultyDepartment of Applied Chemistry
curtin.facultyNanochemistry Research Institute (Research Institute)
curtin.facultySchool of Science
curtin.facultyFaculty of Science and Engineering


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