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

Parallel Molecular Dynamics Code Validation Through Bulk Silicon Thermal Conductivity Calculations

2003 ◽  
Author(s):  
Carlos J. Gomes ◽  
Marcela Madrid ◽  
Cristina H. Amon
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Single Crystals ◽  
Phonon Frequency ◽  
Interatomic Potential ◽  
Dispersion Relations ◽  
Bulk Silicon ◽  
Ghost Cell ◽  
Frequency Spectra ◽  
Parallel Molecular Dynamics

We have implemented a parallel molecular dynamics algorithm, which incorporates the Stillinger-Weber interatomic potential. The code was parallelized using a ghost cell atomic division approach, ensuring scaling with the number of processors and a significant increase in speed with respect to the serial version. The methodology is validated by computing the thermal conductivity and phonon frequency spectra of bulk silicon single crystals for different domain sizes at 1000K. The predicted thermal conductivities are consistent with the experimental value at that temperature. In addition, the phonon frequency spectra capture the properties expected from the dispersion relations for silicon.

scholarly journals Parallel Molecular Dynamics with Irregular Domain Decomposition

2011 ◽  
Vol 10 (4) ◽  
pp. 1071-1088 ◽  
Author(s):  
Mauro Bisson ◽  
Massimo Bernaschi ◽  
Simone Melchionna
Keyword(s):  
Molecular Dynamics ◽  
Blood Flow ◽  
Input Parameter ◽  
Complex Geometries ◽  
Irregular Domain ◽  
Irregular Domains ◽  
Additional Input ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations ◽  
General Method

AbstractThe spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing. Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular shape. In those cases, the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation. In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

2020 ◽  
Vol 87 ◽  
pp. 107301
Author(s):  
Leandro Takeshi Hattori ◽  
Bruna Araujo Pinheiro ◽  
Rafael Bertolini Frigori ◽  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Parallel Molecular Dynamics
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