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ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level
Author(s) -
Marsili Simone,
Signorini Giorgio Federico,
Chelli Riccardo,
Marchi Massimo,
Procacci Piero
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21388
Subject(s) - metadynamics , molecular dynamics , replica , fortran , suite , computational science , computer science , parallel tempering , constant (computer programming) , chemistry , computational chemistry , programming language , art , bayesian probability , archaeology , artificial intelligence , markov chain monte carlo , monte carlo molecular modeling , visual arts , history
We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.