Parallel molecular dynamics simulations of biomolecular systems

1998 ◽  
pp. 296-303 ◽  
Author(s):  
Alexander Lyubartsev ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Parallel Molecular Dynamics ◽  
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.

PARALLEL MOLECULAR DYNAMICS SIMULATIONS OF ORGANIC MATERIALS

1994 ◽  
Vol 05 (02) ◽  
pp. 295-298 ◽  
Author(s):  
STEVE PLIMPTON ◽  
BRUCE HENDRICKSON
Keyword(s):  
Molecular Dynamics ◽  
Parallel Algorithms ◽  
Molecular Dynamics Simulations ◽  
Parallel Algorithm ◽  
Communication Cost ◽  
Dynamics Model ◽  
Organic Systems ◽  
Intel Paragon ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

A new parallel algorithm suitable for molecular dynamics simulations of organic systems is presented. It reduces the communication cost and memory requirements of other commonly-used parallel algorithms by a factor of [Formula: see text] where P is the number of processors. The algorithm has been implemented in a CHARMM-like molecular dynamics model and its performance on 1024-processor nCUBE 2 and Intel Paragon machines is discussed.

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