Potential functions for simulation of biomolecular systems - Introduction

被引:1
作者
Klein, ML [1 ]
Marchi, M [1 ]
Smith, JC [1 ]
机构
[1] CEA SACLAY, SBPM, DBCM, COMMISSARIAT ENERGIE ATOM, F-91191 GIF SUR YVETTE, FRANCE
关键词
simulation; biomolecules; potential functions;
D O I
10.1051/jcp/1997941305
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The basic principles and the inherent problems of deriving potential energy functions for use in simulations of molecular systems are discussed.
引用
收藏
页码:1305 / 1312
页数:8
相关论文
共 38 条
[1]   SOLUTE DIFFUSION IN LIPID BILAYER-MEMBRANES - AN ATOMIC-LEVEL STUDY BY MOLECULAR-DYNAMICS SIMULATION [J].
BASSOLINOKLIMAS, D ;
ALPER, HE ;
STOUCH, TR .
BIOCHEMISTRY, 1993, 32 (47) :12624-12637
[2]   MOLECULAR MECHANICS PARAMETERS FOR ELECTRONICALLY EXCITED-STATES - THE (N, PI-STAR) SINGLET-STATE OF FORMALDEHYDE [J].
BLAIR, JT ;
LEVY, RM ;
KROGHJESPERSEN, K .
CHEMICAL PHYSICS LETTERS, 1990, 166 (04) :429-436
[3]   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
[4]  
BROOKS LC, 1989, PROTEINS THEORETICAL
[5]   UNIFIED APPROACH FOR MOLECULAR-DYNAMICS AND DENSITY-FUNCTIONAL THEORY [J].
CAR, R ;
PARRINELLO, M .
PHYSICAL REVIEW LETTERS, 1985, 55 (22) :2471-2474
[6]   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
[7]   A THEORETICAL-EXAMINATION OF SOLVATOCHROMISM AND SOLUTE SOLVENT STRUCTURING IN SIMPLE ALKYL CARBONYL-COMPOUNDS - SIMULATIONS USING STATISTICAL MECHANICAL FREE-ENERGY PERTURBATION-METHODS [J].
DEBOLT, SE ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1990, 112 (21) :7515-7524
[8]   SIMULATION OF ELECTROSTATIC SYSTEMS IN PERIODIC BOUNDARY-CONDITIONS .1. LATTICE SUMS AND DIELECTRIC-CONSTANTS [J].
DELEEUW, SW ;
PERRAM, JW ;
SMITH, ER .
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 1980, 373 (1752) :27-56
[9]   AN ALL-ELECTRON NUMERICAL-METHOD FOR SOLVING THE LOCAL DENSITY FUNCTIONAL FOR POLYATOMIC-MOLECULES [J].
DELLEY, B .
JOURNAL OF CHEMICAL PHYSICS, 1990, 92 (01) :508-517
[10]   THE DEVELOPMENT AND USE OF QUANTUM-MECHANICAL MOLECULAR-MODELS .76. AM1 - A NEW GENERAL-PURPOSE QUANTUM-MECHANICAL MOLECULAR-MODEL [J].
DEWAR, MJS ;
ZOEBISCH, EG ;
HEALY, EF ;
STEWART, JJP .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1985, 107 (13) :3902-3909