scholarly journals GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

2017 ◽  
Vol 38 (25) ◽  
pp. 2193-2206 ◽  
Author(s):  
Chigusa Kobayashi ◽  
Jaewoon Jung ◽  
Yasuhiro Matsunaga ◽  
Takaharu Mori ◽  
Tadashi Ando ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enhanced Sampling ◽  
Sampling Algorithms ◽  
Parallel Molecular Dynamics

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins

2015 ◽  
Vol 119 (46) ◽  
pp. 14594-14603 ◽  
Author(s):  
Ole Juul Andersen ◽  
Julie Grouleff ◽  
Perri Needham ◽  
Ross C. Walker ◽  
Frank Jensen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Molecular Dynamics Method ◽  
Enhanced Sampling ◽  
Dynamics Method

NAMD2: Greater Scalability for Parallel Molecular Dynamics

1999 ◽  
Vol 151 (1) ◽  
pp. 283-312 ◽  
Author(s):  
Laxmikant Kalé ◽  
Robert Skeel ◽  
Milind Bhandarkar ◽  
Robert Brunner ◽  
Attila Gursoy ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Parallel Molecular Dynamics

SPONGE : A GPU‐Accelerated Molecular Dynamics Package with Enhanced Sampling and AI‐Driven Algorithms

2021 ◽  
Author(s):  
Yu‐Peng Huang ◽  
Yijie Xia ◽  
Lijiang Yang ◽  
Jiachen Wei ◽  
Yi Isaac Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enhanced Sampling ◽  
Accelerated Molecular Dynamics
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