title: Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions.
abstract: A molecular dynamics (MD) simulation program for biological macromolecules was implemented with a non-Ewald scheme for long-ranged electrostatic interactions and run on a general purpose graphics processing unit (GPU). We recently developed several non-Ewald methods to compute the electrostatic energies with high precision. In particular, the zero-dipole summation (ZD) method, which takes into account the neutralities of charges and dipoles in a truncated subset, enables the calculation of electrostatic interactions with high accuracy and low computational cost, and its algorithm is simple enough to be implemented in a GPU. We developed an MD program with the space decomposition algorithm, myPresto/psygene, and applied it to several biological macromolecular systems with GPUs implementing the ZD method. Rapid computing performance with high accuracy was obtained.
authors.affiliation: Japan Biological Informatics Consortium (JBIC), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.|Information and Mathematical Science Bio Inc., Owl Tower, 4-21-1, Higashi-Ikebukuro, Toshima-ku, Tokyo 170-0013, Japan.
authors.forename: Tadaaki
authors.initials: T
authors.lastname: Mashimo
authors.affiliation: Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Yoshifumi
authors.initials: Y
authors.lastname: Fukunishi
authors.affiliation: Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Narutoshi
authors.initials: N
authors.lastname: Kamiya
authors.affiliation: Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.|JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Takano
authors.affiliation: Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Ikuo
authors.initials: I
authors.lastname: Fukuda
authors.affiliation: Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.|Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura