✦ LIBER ✦

Protein calculations on parallel processors. II. Parallel algorithm for the forces and molecular dynamics

✍ Scribed by J.F. Janak; P.C. Pattnaik

Publisher: John Wiley and Sons
Year: 1992
Tongue: English
Weight: 456 KB
Volume: 13
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.540130908

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

We describe two algorithms for the parallel calculation of a CHARMm‐like force field in macromolecules. For a molecule with a given number of atoms, we show that there is an optimal number of processors leading to a minimum computation time. At the optimum, both the number of processors and the computation time are proportional to the number of atoms. © 1992 by John Wiley & Sons, Inc.

📜 SIMILAR VOLUMES

Development of a parallel molecular dyna

Development of a parallel molecular dynamics code on SIMD computers: Algorithm for use of pair list criterion

✍ Roccatano, D.; Bizzarri, R.; Chillemi, G.; Sanna, N.; Di Nola, A. 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 207 KB 👁 3 views

In recent years several implementations of molecular dynamics Ž . Ž . MD codes have been reported on multiple instruction multiple data MIMD machines. However, very few implementations of MD codes on single instruction Ž . multiple data SIMD machines have been reported. The difficulty in using pair

Molecular dynamics for very large system

Molecular dynamics for very large systems on massively parallel computers: The MPSim program

✍ Lim, Kian-Tat; Brunett, Sharon; Iotov, Mihail; McClurg, Richard B.; Vaidehi, Nag 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 377 KB 👁 1 views

We describe the implementation of the cell multipole method CMM in a Ž . Ž . complete molecular dynamics MD simulation program MPSim for massively parallel supercomputers. Tests are made of how the program scales with size Ž . Ž . linearly and with number of CPUs nearly linearly in applications invo