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

Computer Physics Communications

Volumn 180, Issue 10, 2009, Pages 1961-1972

  Bonomi, Massimiliano ^a   Branduardi, Davide ^a   Bussi, Giovanni ^b   Camilloni, Carlo ^c   Provasi, Davide ^d   Raiteri, Paolo ^e   Donadio, Davide ^f   Marinelli, Fabrizio ^g   Pietrucci, Fabio ^g   Broglia, Ricardo A ^c,h   Parrinello, Michele ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^c INFN SEZIONE DI MILANO   (Italy)

^d MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^e NRI   (Australia)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g SISSA   (Italy)

^h UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Free energy; Metadynamics; Molecular dynamics; Proteins; Umbrella sampling

Indexed keywords

BIOLOGICAL PROBLEMS; C LANGUAGE; CATALOGUE IDENTIFIERS; CLASSICAL MOLECULAR DYNAMICS; COLLECTIVE VARIABLES; COMPUTATIONAL RESOURCES; CONDENSED MATTER SYSTEM; DISTRIBUTED PROGRAM; EQUATION BASED; FORTRAN; FREE ENERGY SURFACE; FREE-ENERGY CALCULATIONS; IRELAND; METADYNAMICS; MOLECULAR SYSTEMS; OPERATING SYSTEMS; PLUG-INS; PROGRAMMING LANGUAGE; RUNNING TIME; SAMPLING TECHNIQUE; SOLUTION METHODS; STAND -ALONE; STATE-OF-THE-ART METHODS; TEST DATA; UMBRELLA SAMPLING;

ATOMS; COMPUTATIONAL METHODS; COMPUTER OPERATING SYSTEMS; COMPUTER PROGRAMMING; DYNAMICS; LINGUISTICS; MOLECULAR DYNAMICS; PROBLEM ORIENTED LANGUAGES; PROTEINS; SANDERS; TEST FACILITIES;

FREE ENERGY;

EID: 69349100797     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2009.05.011     Document Type: Article

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