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

• General Information
• Who is behind Orac
• Citation
• Licensing information
• Download
• Release notes
• PrimaDORAC (NEW!)

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 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.

• Read ORAC manual (PDF).
• View a PDF presentation on Performing advanced MD simulations with ORAC
• input examples are provided in the directory tests and include:
  • Basic tests: NVE, NVT, NPT simulations using multiple time steps integration and PME
  • Jarzynski/Crooks tests: non equilibrium driven trajectories on bond and/or bend and/or torsional user-selected coordinates
  • Replica Exchange tests: Applications of standard H-REM algorithm, torsional tempering and solute tempering schemes
  • Serial Generalized Ensemble tests: Applications of SGE schemes
  • Metadynamics tests: Self Healing Umbrella Sampling and well tempered metadynamics applications.
  • Alchemy tests: Non equilibrium alchemical annihilation/creation of organic molecules in explicit solvent.

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

Who is behind Orac

• The main authors of the code are Massimo Marchi (CEA, Saclay, Paris, FR) and Piero Procacci (Florence University, IT)

• Contributors are Simone Marsili (CNIO, Madrid ES), Giorgio F. Signorini, Riccardo Chelli (Florence University, IT), Tom Darden (NIEH, Triangle Park NC, USA), Marc Souaille (University of Evry, FR) and Emanuele Paci (University of Leeds, UK)

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.

• Download now:
  • the latest OpenMP/MPI release (6.2)
  • old release (5.4.1)
  • PrimaDORAC stand-alone f90 source for tpg assignment
  • Tests bundle for running HREM with torsional tempering on POPC model membrane (NPT ensemble with semi-isotropic stress)
  • Full output reference PARxxxx dirs for POPC HREM simulation
• To unpack the archive, move it to a suitable directory and type: tar -zxvf orac.x_y_z.tar.gz
• Building instructions

Releases 5.x are no longer supported

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