THE CALCULATION OF THE POTENTIAL OF MEAN FORCE USING COMPUTER-SIMULATIONS

被引：1423

作者：

ROUX, B

机构：

[1] Université de Montréal, Physics Department, Montréal, H3C 3J7, C.P. 6128, succ. Centre-Ville

来源：

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

关键词：

COMPUTER SIMULATIONS; UMBRELLA SAMPLING; FREE ENERGY SURFACE; POTENTIAL OF MEAN FORCE; ALANINE DIPEPTIDE;

D O I：

10.1016/0010-4655(95)00053-I

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

The problem of unbiasing and combining the results of umbrella sampling calculations is reviewed. The weighted histogram analysis method (WHAM) of S. Kumar et al. (J. Comp. Chem. 13 (1992) 1011) is described and compared with other approaches. The method is illustrated with molecular dynamics simulations of the alanine dipeptide for one- and two-dimensional free energy surfaces. The results show that the WHAM approach simplifies considerably the task of recombining the various windows in complex systems.

引用

收藏

页码：275 / 282

页数：8

相关论文

共 19 条

[1] EFFICIENT ESTIMATION OF FREE-ENERGY DIFFERENCES FROM MONTE-CARLO DATA [J].

BENNETT, CH .

JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (02) :245-268

[2] THE COMPUTATION OF A POTENTIAL OF MEAN FORCE - CHOICE OF THE BIASING POTENTIAL IN THE UMBRELLA SAMPLING TECHNIQUE [J].

BEUTLER, TC ;

VANGUNSTEREN, WF .

JOURNAL OF CHEMICAL PHYSICS, 1994, 100 (02) :1492-1497

[3] CONSTANT-TEMPERATURE FREE-ENERGY SURFACES FOR PHYSICAL AND CHEMICAL PROCESSES [J].

BOCZKO, EM ;

BROOKS, CL .

JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (17) :4509-4513

[4] CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].

BROOKS, BR ;

BRUCCOLERI, RE ;

OLAFSON, BD ;

STATES, DJ ;

SWAMINATHAN, S ;

KARPLUS, M .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217

[5] PROMOTION OF HELIX FORMATION IN PEPTIDES DISSOLVED IN ALCOHOL AND WATER-ALCOHOL MIXTURES [J].

BROOKS, CL ;

NILSSON, L .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (23) :11034-11035

[6] STATISTICAL-MECHANICS OF ISOMERIZATION DYNAMICS IN LIQUIDS AND TRANSITION-STATE APPROXIMATION [J].

CHANDLER, D .

JOURNAL OF CHEMICAL PHYSICS, 1978, 68 (06) :2959-2970

[7] A MOLECULAR-DYNAMICS STUDY OF GATING IN DIOXOLANE-LINKED GRAMICIDIN-A CHANNELS [J].

CROUZY, S ;

WOOLF, TB ;

ROUX, B .

BIOPHYSICAL JOURNAL, 1994, 67 (04) :1370-1386

[8] OPTIMIZED MONTE-CARLO DATA-ANALYSIS [J].

FERRENBERG, AM ;

SWENDSEN, RH .

PHYSICAL REVIEW LETTERS, 1989, 63 (12) :1195-1198

[9] TRYPTOPHAN-47 ROTATIONAL ISOMERIZATION IN VARIANT-3 SCORPION NEUROTOXIN - A COMBINATION THERMODYNAMIC PERTURBATION AND UMBRELLA SAMPLING STUDY [J].

HAYDOCK, C ;

SHARP, JC ;

PRENDERGAST, FG .

BIOPHYSICAL JOURNAL, 1990, 57 (06) :1269-1279

[10] COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER [J].

JORGENSEN, WL ;

CHANDRASEKHAR, J ;

MADURA, JD ;

IMPEY, RW ;

KLEIN, ML .

JOURNAL OF CHEMICAL PHYSICS, 1983, 79 (02) :926-935