Adventures in improving the scaling and accuracy of a parallel molecular dynamics program

被引：95

作者：

Crowley, MF ^{[1
]}

Darden, TA ^{[1
]}

Cheatham, TE ^{[1
]}

Deerfield, DW ^{[1
]}

机构：

[1] NIEHS, RES TRIANGLE PK, NC 27709 USA

来源：

JOURNAL OF SUPERCOMPUTING | 1997年 / 11卷 / 03期

关键词：

Ewald; parallel; T3E; simulation; electrostatic; molecular dynamics; PME;

D O I：

10.1023/A:1007907925007

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

We report our work to parallelize the Particle Mesh Ewald (PME) method to compute the long-range electrostatic interactions in the molecular dynamics program AMBER and to extend the scalability of the PME method to hundreds of processors.

引用

页码：255 / 278

页数：24

共 20 条

[1]

BROOKS CL, 1990, NATO ADV SCI I C-MAT, V293, P289

[2]

Cheatham TE, 1996, J MOL BIOL, V259, P434

[3]

CHEATHAM TE, 1997, IN PRESS PROT NUC AC

[4] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].

CORNELL, WD ;

CIEPLAK, P ;

BAYLY, CI ;

GOULD, IR ;

MERZ, KM ;

FERGUSON, DM ;

SPELLMEYER, DC ;

FOX, T ;

CALDWELL, JW ;

KOLLMAN, PA .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197

[5] PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].

DARDEN, T ;

YORK, D ;

PEDERSEN, L .

JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092

[6] A SMOOTH PARTICLE MESH EWALD METHOD [J].

ESSMANN, U ;

PERERA, L ;

BERKOWITZ, ML ;

DARDEN, T ;

LEE, H ;

PEDERSEN, LG .

JOURNAL OF CHEMICAL PHYSICS, 1995, 103 (19) :8577-8593

[7] PARTICLE-MESH METHODS ON THE CONNECTION MACHINE [J].

FERRELL, R ;

BERTSCHINGER, E .

INTERNATIONAL JOURNAL OF MODERN PHYSICS C-PHYSICS AND COMPUTERS, 1994, 5 (06) :933-956

[8] A FAST ALGORITHM FOR PARTICLE SIMULATIONS [J].

GREENGARD, L ;

ROKHLIN, V .

JOURNAL OF COMPUTATIONAL PHYSICS, 1987, 73 (02) :325-348

[9]

GREENGARD L, 1985, J COMPUT PHYS, V60, P187

[10]

HOCKNEY RW, 1981, COMPUTER SIMULATION

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