TY - JOUR
T1 - Accelerated molecular dynamics simulation with the parallel fast multipole algorithm
AU - Board, John A.
AU - Causey, Jeffrey W.
AU - Leathrum, James F.
AU - Windemuth, Andreas
AU - Schulten, Klaus
N1 - Funding Information:
JAB and JFL were supported by the NSF. JWC was an undergraduate fellow of the Duke/NSF Engineering Research Center. AW and KS were supported by the National Institute of Health (grant P41RRO5969). We also thank the staff of the National Center for Supercomputing Applications for providing computational resources and the staff of Scientific Computing Associates, notably Tim Mattson, for generously providing advice about Linda.
PY - 1992/10/2
Y1 - 1992/10/2
N2 - We have implemented the fast multipole algorithm (FMA) of Greengard and Rokhlin and incorporated it into the molecular dynamics program MD of Windemuth and Schulten, allowing rapid computation of the non-bonded forces acting in dynamical protein systems without truncation or other corruption of the Coulomb force. The resulting program speeds up simulations of protein systems with approximately 24000 atoms by up to an order of magnitude on a single workstation. Additionally, we have implemented a parallel version of the three-dimensional FMA code on a loosely coupled workstations, further reducing simulation times. Large (in both size of system and length of simulated time) protein molecular dynamics simulations are now possible on workstations rather than supercomputers, and very large protein computations are possible on clusters of workstations and parallel machines.
AB - We have implemented the fast multipole algorithm (FMA) of Greengard and Rokhlin and incorporated it into the molecular dynamics program MD of Windemuth and Schulten, allowing rapid computation of the non-bonded forces acting in dynamical protein systems without truncation or other corruption of the Coulomb force. The resulting program speeds up simulations of protein systems with approximately 24000 atoms by up to an order of magnitude on a single workstation. Additionally, we have implemented a parallel version of the three-dimensional FMA code on a loosely coupled workstations, further reducing simulation times. Large (in both size of system and length of simulated time) protein molecular dynamics simulations are now possible on workstations rather than supercomputers, and very large protein computations are possible on clusters of workstations and parallel machines.
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U2 - 10.1016/0009-2614(92)90053-P
DO - 10.1016/0009-2614(92)90053-P
M3 - Article
AN - SCOPUS:5544323152
SN - 0009-2614
VL - 198
SP - 89
EP - 94
JO - Chemical Physics Letters
JF - Chemical Physics Letters
IS - 1-2
ER -