Biophysics and Physicobiology | |
myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling | |
Takuya Takahashi1  Kota Kasahara1  Satoshi Goto2  Hiroki Terazawa2  Hayato Itaya2  Junichi Higo3  Haruki Nakamura4  | |
[1] College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan;Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan;Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan;Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; | |
关键词: molecular simulation; software; generalized ensemble; high performance computing; gpgpu; | |
DOI : 10.2142/biophysico.BSJ-2020013 | |
来源: DOAJ |
【 摘 要 】
The molecular dynamics (MD) method is a promising approach for investigating the molecular mechanisms of microscopic phenomena. In particular, generalized ensemble MD methods can efficiently explore the conformational space with a rugged free-energy surface. However, the implementation and acquisition of technical knowledge for each generalized ensemble MD method are not straightforward for end-users. Here, we present a new version of the myPresto/omegagene software, which is an MD simulation engine tailored for a series of generalized ensemble methods, which are virtual-system coupled multicanonical MD (V-McMD), virtual-system coupled adaptive umbrella sampling (V-AUS), and virtual-system coupled canonical MD (VcMD). This program has been applied in several studies analyzing free-energy landscapes of a variety of molecular systems with all-atom simulations. The updated version provides new functionality for coarse-grained simulations powered by the hydrophobicity scale method. The software package includes a step-by-step tutorial document for enhanced conformational sampling of the poly-glutamine (poly-Q) oligomer expressed as a one-bead per residue model. The myPresto/omegagene software is freely available at the following URL: https://github.com/kotakasahara/omegagene under the Apache2 license.
【 授权许可】
Unknown