### Abstract

Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.

Original language | English (US) |
---|---|

Pages (from-to) | 1022-1035 |

Number of pages | 14 |

Journal | Journal of Computational Chemistry |

Volume | 13 |

Issue number | 8 |

DOIs | |

State | Published - 1992 |

Externally published | Yes |

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### ASJC Scopus subject areas

- Chemistry(all)
- Computational Mathematics

### Cite this

*Journal of Computational Chemistry*,

*13*(8), 1022-1035. https://doi.org/10.1002/jcc.540130813

**Molecular dynamics on a distributed‐memory multiprocessor.** / Lin, S. L.; Mellor‐Crummey, J.; Pettitt, Bernard; Phillips, G. N.

Research output: Contribution to journal › Article

*Journal of Computational Chemistry*, vol. 13, no. 8, pp. 1022-1035. https://doi.org/10.1002/jcc.540130813

}

TY - JOUR

T1 - Molecular dynamics on a distributed‐memory multiprocessor

AU - Lin, S. L.

AU - Mellor‐Crummey, J.

AU - Pettitt, Bernard

AU - Phillips, G. N.

PY - 1992

Y1 - 1992

N2 - Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.

AB - Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.

UR - http://www.scopus.com/inward/record.url?scp=0007036955&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0007036955&partnerID=8YFLogxK

U2 - 10.1002/jcc.540130813

DO - 10.1002/jcc.540130813

M3 - Article

VL - 13

SP - 1022

EP - 1035

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 8

ER -