ORAC (release 6) - An OpenMP/MPI molecular dynamics engine to simulate solvated biomolecules



General Information

This is release 6 (started 2014) of the ORAC engine, a FORTRAN suite to simulate at the atomistic level complex biosystems. The release 4 (4.0) of the ORAC code [ J. Comput. Chem. 18:1834-1862, 1997 ] included multiple time steps integration, Smooth Particle Mesh Ewald method, constant pressure and constant temperature simulations. Release 5 ( J. Comp. Chem. 31:1106:1116, 2010 ) was supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics on multidimensional reaction coordinates subspaces, and potential of mean force reconstruction along arbitrary reaction paths using non equilibrium molecular dynamics techniques. All these computational technologies have been implemented on parallel architectures using the standard MPI communication protocol. In Release 6 ORAC implements a weak scaling parallel algorithm via MPI calls in H-REM/SGE generalized ensemble simulations or driven simulations technologies based on nonequilibrium theorem and a strong scaling parallel approach on the OpenMP layer based on particle decomposition for the computation of the forces.

ORAC is an open-source program distributed free of charge under the GNU general public license (GPL).


Who is behind Orac


Citation

orac6.x citation:

      P. Procacci
      "Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program
       for Generalized Ensemble and Fast Switching Alchemical Simulations"
      J. Chem. Inf. Model., 2016, 56 (6), pp 1117-1121
    

Please use the following citations when publishing results obtained with orac5.x:

      P. Procacci, E. Paci, T. Darden, M. Marchi
      "ORAC: A Molecular Dynamics Program to Simulate
      Complex Molecular Systems with Realistic Electrostatic Interactions"
      J. Comp. Chemistry, 18, No. 15 1848-1862 (1997).
    

      S. Marsili, G. F. Signorini, R. Chelli, M. Marchi and P. Procacci 
      "Orac: A molecular dynamics simulation program 
      to explore free energy surfaces in biomolecular systems at the atomistic level."
      J. Comp. Chemistry, 31, No. 5 1106-1116 (2010) 
    


Licensing information

The ORAC program is free software and is distributed free of charge; you can redistribute it and/or modify it under the terms of the GNU General Public License (GPL). There is no warranty for the program and no professional support is provided. Bugs are fixed at the authors' earliest convenience, upon request to the E-mail address piero.procacci@unifi.it. Read carefully the GPL TERMS AND CONDITIONS FOR USE, DISTRIBUTION AND MODIFICATION prior to downloading.


Download

Orac is available only for UNIX operating systems as a tar archive at this site.

Release 5.0 is no longer supported


PrimaDORAC

PrimaDORAC is a free web interface for the assignment of partial charges, chemical topology and bonded parameters in organic or drug molecules.
The interface relies on our in-house FORTRAN90 parser, working on the recently released Generalized Amber Force Field parameter set (GAFF2). AM1/BCC charges are computed using the Public Domain version of the MOPAC7 program and the bond charge corrections (BCC) reported in Ref. Jakalian et al , J Comp Chem, 2002, 23, 1623-1641. The interface has been tested on about 60000 compounds (identified with a CAS-registry number) taken from the National Cancer Institute (NCI) Open Database, producing GAFF2 minimized structures bearing a mean Root Square Displacement of about 0.01 nm respect to the original CORINA generated 3D NCI structures.
This project has been partially funded by Regione Toscana.

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