OPALp: Difference between revisions
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== References == | == References == | ||
* Koradi, R., Billeter, M. & Güntert, P. Point-centered domain decomposition for parallel molecular dynamics simulation. | * Koradi, R., Billeter, M. & Güntert, P. Point-centered domain decomposition for parallel molecular dynamics simulation. [http://dx.doi.org/10.1016/S0010-4655(99)00436-1 Comp. Phys. Commun. 124, 139–147 (2000)] | ||
Revision as of 14:37, 15 June 2009
Energy refinement and molecular dynamics simulation algorithm for biomolecules
OPALp is a program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules. OPALp features point-centered domain decomposition, a new algorithm for MD simulations on parallel computers that can make efficient use of up to 100 and more processors for realistic systems of a protein in water comprising 10 000 to 20 000 atoms. The implementation in OPALp uses a standard message passing library, so that the program runs on both shared memory and massively parallel distributed memory computers.
Availability
- Development and support for OPALp has been stopped. The program is currently not available.
References
- Koradi, R., Billeter, M. & Güntert, P. Point-centered domain decomposition for parallel molecular dynamics simulation. Comp. Phys. Commun. 124, 139–147 (2000)