The GROMOS biomolecular simulation program package

被引：1289

作者：

Scott, WRP ^{[1
]}

Hünenberger, PH ^{[1
]}

Tironi, IG ^{[1
]}

Mark, AE ^{[1
]}

Billeter, SR ^{[1
]}

Fennen, J ^{[1
]}

Torda, AE ^{[1
]}

Huber, T ^{[1
]}

Krüger, P ^{[1
]}

van Gunsteren, WF ^{[1
]}

机构：

[1] ETH Zentrum, Phys Chem Lab, CH-8092 Zurich, Switzerland

来源：

JOURNAL OF PHYSICAL CHEMISTRY A | 1999年 / 103卷 / 19期

关键词：

D O I：

10.1021/jp984217f

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We present the newest version of the GROningen MOlecular Simulation program package, GROMOS96. GROMOS96 has been developed for the dynamic modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization as well as the path-integral formalism. An overview of its functionality is given, highlighting methodology not present in the last major release, GROMOS87. The organization of the code is outlined and reliability, testing, and efficiency issues involved in the design of this large (73 000 lines of FORTRAN77 code) and complex package are discussed. Finally, we present two applications illustrating new functionality: local elevation simulation and molecular dynamics in four spatial dimensions.

引用

页码：3596 / 3607

页数：12

共 32 条

[1] MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].

BERENDSEN, HJC ;

POSTMA, JPM ;

VANGUNSTEREN, WF ;

DINOLA, A ;

HAAK, JR .

JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690

[2]

Berendsen HJC, 1985, MOL DYNAMICS PROTEIN, P18

[3] PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES [J].

BERNSTEIN, FC ;

KOETZLE, TF ;

WILLIAMS, GJB ;

MEYER, EF ;

BRICE, MD ;

RODGERS, JR ;

KENNARD, O ;

SHIMANOUCHI, T ;

TASUMI, M .

JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) :535-542

[4] AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS [J].

BEUTLER, TC ;

MARK, AE ;

VANSCHAIK, RC ;

GERBER, PR ;

VANGUNSTEREN, WF .

CHEMICAL PHYSICS LETTERS, 1994, 222 (06) :529-539

[5] MOLECULAR-DYNAMICS FREE-ENERGY CALCULATION IN 4 DIMENSIONS [J].

BEUTLER, TC ;

VANGUNSTEREN, WF .

JOURNAL OF CHEMICAL PHYSICS, 1994, 101 (02) :1417-1422

[6] CAN THE DENSITY MAXIMUM OF WATER BE FOUND BY COMPUTER-SIMULATION [J].

BILLETER, SR ;

KING, PM ;

VANGUNSTEREN, WF .

JOURNAL OF CHEMICAL PHYSICS, 1994, 100 (09) :6692-6699

[7] EXPLOITING THE ISOMORPHISM BETWEEN QUANTUM-THEORY AND CLASSICAL STATISTICAL-MECHANICS OF POLYATOMIC FLUIDS [J].

CHANDLER, D ;

WOLYNES, PG .

JOURNAL OF CHEMICAL PHYSICS, 1981, 74 (07) :4078-4095

[8]

Daura X, 1998, J COMPUT CHEM, V19, P535, DOI 10.1002/(SICI)1096-987X(19980415)19:5<535::AID-JCC6>3.0.CO

[9]

2-N

[10]

FEYNMAN RP, 1965, PATH INTEGRALS QUANT

← 1 2 3 4 →