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.

PLUMED: A portable plugin for free-energy calculations with molecular dynamics / Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello, M.. - 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

Bussi, G.;
2009-01-01

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.
2009
180
10
1961
1972
https://arxiv.org/abs/0902.0874
Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello,...espandi
File in questo prodotto:
File Dimensione Formato  
sdarticle.pdf

non disponibili

Tipologia: Versione Editoriale (PDF)
Licenza: Non specificato
Dimensione 485.33 kB
Formato Adobe PDF
485.33 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/12498
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 1367
  • ???jsp.display-item.citation.isi??? 1347
social impact