Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

@article{citeulike:3000713, abstract = {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. {\copyright} 2008 Wiley Periodicals, Inc. J Comput Chem 2008}, address = {Advanced Center for Computing and Communication, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Center for Advanced Medical Engineering and Informatics, Open Laboratories for Advanced Biosicence and Biotechnology, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; High Performance Biocomputing Research Team, Bioinformatics Group, Genomic, Sciences Center, RIKEN, 61-1 Onocho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan}, author = {Kikugawa, Gota and Apostolov, Rossen and Kamiya, Narutoshi and Taiji, Makoto and Himeno, Ryutaro and Nakamura, Haruki and Yonezawa, Yasushige }, citeulike-article-id = {3000713}, doi = {10.1002/jcc.21035}, journal = {Journal of Computational Chemistry}, keywords = {md}, number = {9999}, pages = {NA+}, posted-at = {2008-07-15 02:43:13}, priority = {2}, title = {Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems}, url = {http://dx.doi.org/10.1002/jcc.21035}, volume = {9999}, year = {2008} }

TY - JOUR ID - citeulike:3000713 L3 - citeulike-article-id:3000713 TI - Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems JF - Journal of Computational Chemistry VL - 9999 IS - 9999 SP - NA AD - Advanced Center for Computing and Communication, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Center for Advanced Medical Engineering and Informatics, Open Laboratories for Advanced Biosicence and Biotechnology, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; High Performance Biocomputing Research Team, Bioinformatics Group, Genomic, Sciences Center, RIKEN, 61-1 Onocho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan N2 - 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. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 KW - md AU - Kikugawa, Gota AU - Apostolov, Rossen AU - Kamiya, Narutoshi AU - Taiji, Makoto AU - Himeno, Ryutaro AU - Nakamura, Haruki AU - Yonezawa, Yasushige PY - 2008/// UR - http://dx.doi.org/10.1002/jcc.21035 ER -