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Application of MDGRAPE-3, a Special Purpose Board for Molecular Dynamics Simulations, to Periodic Biomolecular Systems
Osaka University.
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2009 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 30, no 1, 110-118 p.Article in journal (Refereed) Published
Abstract [en]

We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.

Place, publisher, year, edition, pages
2009. Vol. 30, no 1, 110-118 p.
Keyword [en]
high-performance computing, special-purpose computer, cutoff method, Ewald method, MDGRAPE-3
National Category
Bioinformatics and Systems Biology Theoretical Chemistry
URN: urn:nbn:se:kth:diva-83200DOI: 10.1002/jcc.21035ISI: 000261907000012PubMedID: 18524021OAI: diva2:501396
QC 20120214Available from: 2012-02-14 Created: 2012-02-12 Last updated: 2012-02-14Bibliographically approved

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Apostolov, Rossen
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