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

2009 ◽  
Vol 30 (1) ◽  
pp. 110-118 ◽  
Author(s):  
Gota Kikugawa ◽  
Rossen Apostolov ◽  
Narutoshi Kamiya ◽  
Makoto Taiji ◽  
Ryutaro Himeno ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Dynamics Simulations

scholarly journals Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems

2015 ◽  
Vol 17 (15) ◽  
pp. 9959-9972 ◽  
Author(s):  
Juan Torras
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Active Zones ◽  
Dynamics Simulations

A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented.

scholarly journals Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

2018 ◽  
Vol 14 (12) ◽  
pp. 6748-6749 ◽  
Author(s):  
Brian K. Radak ◽  
Christophe Chipot ◽  
Donghyuk Suh ◽  
Sunhwan Jo ◽  
Wei Jiang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Constant Ph ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics

scholarly journals Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

2017 ◽  
Vol 13 (12) ◽  
pp. 5933-5944 ◽  
Author(s):  
Brian K. Radak ◽  
Christophe Chipot ◽  
Donghyuk Suh ◽  
Sunhwan Jo ◽  
Wei Jiang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Constant Ph ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics

scholarly journals Scalable Molecular Dynamics for Large Biomolecular Systems

2000 ◽  
Vol 8 (3) ◽  
pp. 195-207 ◽  
Author(s):  
Robert K. Brunner ◽  
James C. Phillips ◽  
Laxmikant V. Kalé
Keyword(s):  
Molecular Dynamics ◽  
Load Balancing ◽  
Molecular Dynamics Simulations ◽  
Production Quality ◽  
Biomolecular Systems ◽  
Spatial Decomposition ◽  
Decomposition Scheme ◽  
Object Based ◽  
Dynamics Simulations ◽  
Performance Results

We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

scholarly journals New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

2018 ◽  
Vol 20 (13) ◽  
pp. 8432-8449 ◽  
Author(s):  
Jejoong Yoo ◽  
Aleksei Aksimentiev
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Biomolecular Systems ◽  
Recent Advances ◽  
Dynamics Simulations

Recent advances in parallel computing have pushed all-atom molecular dynamics simulations into an untested territory. This article reviews the applications of the NBFIX approach for testing and improving molecular dynamics force fields and discuses the implications of the NBFIX corrections for simulations of various biomolecular systems.

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