myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme-Reference-Cited by-同舟云学术

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme

Published:2016 Issue:0 Volume:13 Page:209-216
ISSN:2189-4779
Container-title:Biophysics and Physicobiology
language:en
Short-container-title:BIOPHYSICS

Author:

Kasahara Kota¹,Ma Benson²,Goto Kota³,Dasgupta Bhaskar⁴⁵,Higo Junichi⁴,Fukuda Ikuo⁴,Mashimo Tadaaki⁵,Akiyama Yutaka³⁶,Nakamura Haruki⁴

Affiliation:

1. College of Life Sciences, Ritsumeikan University

2. College of Engineering, University of Illinois

3. School of Computing, Tokyo Institute of Technology

4. Institute for Protein Research, Osaka University

5. Technology Research Association for Next Generation Natural Products Chemistry

6. Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology

Publisher

Biophysical Society of Japan

Subject

General Medicine

Link

https://www.jstage.jst.go.jp/article/biophysico/13/0/13_209/_pdf

Reference29 articles.

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2. [6] Páll, S. & Hess, B. A flexible algorithm for calculating pair interactions on SIMD architectures. Comput. Phys. Commun. 184, 2641–2650 (2013).

3. [10] Mori, T., Jung, J. & Sugita, Y. Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems. J. Chem. Theory Comput. 9, 5629–5640 (2013).

4. [11] Jung, J., Mori, T. & Sugita, Y. Efficient lookup table using a linear function of inverse distance squared. J. Comput. Chem. 34, 2412–2420 (2013).

5. [12] Jung, J., Mori, T. & Sugita, Y. Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. J. Comput. Chem. 35, 1064–1072 (2014).

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