MOIL - A PROGRAM FOR SIMULATIONS OF MACROMOLECULES

被引：144

作者：

ELBER, R

ROITBERG, A

SIMMERLING, C

GOLDSTEIN, R

LI, HY

VERKHIVKER, G

KEASAR, C

ZHANG, J

ULITSKY, A

机构：

[1] HEBREW UNIV JERUSALEM,FRITZ HABER RES CTR,DEPT CHEM PHYS,IL-91904 JERUSALEM,ISRAEL

[2] HEBREW UNIV JERUSALEM,INST LIFE SCI,IL-91904 JERUSALEM,ISRAEL

[3] NORTHWESTERN UNIV,DEPT CHEM,EVANSTON,IL 60208

[4] UNIV CALIF SAN FRANCISCO,DEPT PHARMACEUT CHEM,SAN FRANCISCO,CA 94143

[5] BIOSYM TECHNOL INC,SAN DIEGO,CA 90089

[6] AGOURON PHARMACEUT INC,SAN DIEGO,CA 92121

[7] CORNELL UNIV,DEPT BIOCHEM MOLEC & CELL BIOL,ITHACA,NY 14853

来源：

COMPUTER PHYSICS COMMUNICATIONS | 1995年 / 91卷 / 1-3期

关键词：

MOLECULAR DYNAMICS; MODELING; ENERGY MINIMIZATION; REACTION PATHS; CURVE CROSSING; LIBRARY OF SIMULATION PROGRAMS;

D O I：

10.1016/0010-4655(95)00047-J

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

A package of computer programs for molecular dynamics simulations-MOIL-is described. A flexible data structure enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field. The supplied parameter set has proteins in mind. In addition to 'wide spread' applications such as energy, energy minimization, normal modes, dynamics and free energy calculations code is also provided to pursue less common applications. This includes reaction path calculations (in condensed phases), uses of the mean field approach for enhanced sampling (LES-locally enhanced sampling) and calculations of curve crossing using the Landau-Zener model. A brief review of the overall program is provided. A few modules are discussed in considerable detail.

引用

页码：159 / 189

页数：31

共 27 条

[1] RATTLE - A VELOCITY VERSION OF THE SHAKE ALGORITHM FOR MOLECULAR-DYNAMICS CALCULATIONS [J].