OPALp

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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.

References

• Koradi, R., Billeter, M. & Güntert, P. Point-centered domain decomposition for parallel molecular dynamics simulation. Comput. Phys. Commun. 124, 139-147 (2000).