Title :
A Monte Carlo approach for processor allocation in molecular dynamics simulations
Author :
Ballestrero, P. ; Ruggiero, C.
Author_Institution :
DIST, Genoa Univ., Italy
Abstract :
A Monte Carlo algorithm for optimal processor allocation for Molecular Dynamics simulations of proteins on Single Instruction Multiple Data flow computer is presented. The algorithm starts from a conventional data structure based on space decomposition algorithm and produces a modified structure based on the atom decomposition approach, optimised in term of computation and communication time. The authors´ approach is well suited for Molecular Dynamics simulations on massively parallel computers based on square or cubic communication networks
Keywords :
Monte Carlo methods; biology computing; digital simulation; molecular biophysics; molecular dynamics method; proteins; Monte Carlo algorithm; atom decomposition approach; communication time; cubic communication networks; massively parallel computers; molecular dynamics simulations; optimal processor allocation; protein dynamics; single instruction multiple data flow computer; space decomposition algorithm; square communication networks; Communication networks; Computational modeling; Computer aided instruction; Computer networks; Computer simulation; Concurrent computing; Data flow computing; Data structures; Monte Carlo methods; Proteins;
Conference_Titel :
Engineering in Medicine and Biology Society, 1994. Engineering Advances: New Opportunities for Biomedical Engineers. Proceedings of the 16th Annual International Conference of the IEEE
Conference_Location :
Baltimore, MD
Print_ISBN :
0-7803-2050-6
DOI :
10.1109/IEMBS.1994.415270
