Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.
Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.
Shifman
M A
MA
Center for Medical Informatics, Yale University School of Medicine, New Have, CT 06510.
Windemuth
A
A
Schulten
K
K
Miller
P L
PL
D000465:Algorithms; D003195:Computer Communication Networks; D003198:Computer Simulation; D008838:Microcomputers; D008968:Molecular Conformation; D011381:Programming Languages; D011487:Protein Conformation; D012984:Software; D013816:Thermodynamics