title: myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.
abstract: Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods,e.g., the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/.
authors.affiliation: College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
authors.forename: Kota
authors.initials: K
authors.lastname: Kasahara
authors.affiliation: College of Engineering, University of Illinois, Urbana-Champaign, United States.
authors.forename: Benson
authors.initials: B
authors.lastname: Ma
authors.affiliation: School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
authors.forename: Kota
authors.initials: K
authors.lastname: Goto
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; Technology Research Association for Next Generation Natural Products Chemistry, Tokyo 135-0064, Japan.
authors.forename: Bhaskar
authors.initials: B
authors.lastname: Dasgupta
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Junichi
authors.initials: J
authors.lastname: Higo
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Ikuo
authors.initials: I
authors.lastname: Fukuda
authors.affiliation: Technology Research Association for Next Generation Natural Products Chemistry, Tokyo 135-0064, Japan.
authors.forename: Tadaaki
authors.initials: T
authors.lastname: Mashimo
authors.affiliation: School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan; Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
keywords: GPGPU; generalized ensemble; high performance computing; molecular simulation; software