Orac (MD program)

Orac
Orac
Original authors	Massimo Marchi, Piero Procacci
Developers	CEA, Saclay, Paris, FR; Florence University, IT
Initial release	1990; 35 years ago
Stable release	5.4.1 / 2010; 15 years ago
Preview release	6.0 / 2016; 9 years ago
Written in	Fortran
Operating system	Unix, Linux
Platform	IA-32, x86-64, NUMA
Available in	English
Type	Molecular dynamics
License	GPL
Website	www.chim.unifi.it/orac

In computer software, Orac is a classical molecular dynamics program, to simulate complex molecular systems at the atomistic level. In 1989-1990, the code was written originally by Massimo Marchi during his stay at International Business Machines (IBM), Kingston (USA). In 1995, the code was developed further at the Centre européen de calcul atomique et moléculaire (CECAM). It is written in the programming language Fortran. In 1997, it was released under a GNU General Public License (GPL).^[1] The latest release ^[2] of Orac may be run in parallel using the standard Message Passing Interface (MPI) libraries, allowing replica exchange simulations, multiple walkers metadynamics^[3] simulations and multiple steered molecular dynamics^[4] nonequilibrium trajectories.

References

^ Procacci, P.; Darden, T.A.; Paci, E.; Marchi, M. (1997). "ORAC: A Molecular Dynamics Program to Simulate Complex Molecular Systems with Realistic Electrostatic Interactions". Journal of Computational Chemistry. 18 (15): 1848–1862. CiteSeerX 10.1.1.554.895. doi:10.1002/(SICI)1096-987X(19971130)18:15<1848::AID-JCC2>3.0.CO;2-O.
^ Marsili, S.; Signorini, G.F.; Chelli, R.; Marchi, M.; Procacci, P. (2010). "ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level". Journal of Computational Chemistry. 31 (5): 1106–1116. doi:10.1002/jcc.21388. PMID 19824035.
^ Laio, A.; Gervasio, F. L. (2008). "Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science". Reports on Progress in Physics. 71 (12) 126601. Bibcode:2008RPPh...71l6601L. doi:10.1088/0034-4885/71/12/126601.
^ Isralewitz, B.; Gao, M.; Schulten, K. (2001). "Steered molecular dynamics and mechanical functions of proteins". Current Opinion in Structural Biology. 11 (2): 224–230. doi:10.1016/S0959-440X(00)00194-9. PMID 11297932.

External links

Official website, Università di Firenze, IT

[1] Procacci, P.; Darden, T.A.; Paci, E.; Marchi, M. (1997). "ORAC: A Molecular Dynamics Program to Simulate Complex Molecular Systems with Realistic Electrostatic Interactions". Journal of Computational Chemistry. 18 (15): 1848–1862. CiteSeerX 10.1.1.554.895. doi:10.1002/(SICI)1096-987X(19971130)18:15<1848::AID-JCC2>3.0.CO;2-O.

[2] Marsili, S.; Signorini, G.F.; Chelli, R.; Marchi, M.; Procacci, P. (2010). "ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level". Journal of Computational Chemistry. 31 (5): 1106–1116. doi:10.1002/jcc.21388. PMID 19824035.

[3] Laio, A.; Gervasio, F. L. (2008). "Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science". Reports on Progress in Physics. 71 (12) 126601. Bibcode:2008RPPh...71l6601L. doi:10.1088/0034-4885/71/12/126601.

[4] Isralewitz, B.; Gao, M.; Schulten, K. (2001). "Steered molecular dynamics and mechanical functions of proteins". Current Opinion in Structural Biology. 11 (2): 224–230. doi:10.1016/S0959-440X(00)00194-9. PMID 11297932.

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