Dual-topology/dual-coordinate free-energy simulation using QM/MM force field

被引：31

作者：

Hu, H ^{[1
]}

Yang, WT ^{[1
]}

机构：

[1] Duke Univ, Dept Chem, Durham, NC 27708 USA

来源：

JOURNAL OF CHEMICAL PHYSICS | 2005年 / 123卷 / 04期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1063/1.1990113

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 have developed a dual-topology/dual-coordinate free-energy simulation method for use with a QM/MM force field. By combining two parallel processes into one alchemical process, we are able to compute the double free-energy difference (Delta Delta F) within a single simulation, which eliminates half of the expensive quantum-mechanical simulation in general. The method has been tested in computing the solvation free-energy differences of several molecular pairs and shows close agreement with experimental results. (C) 2005 American Institute of Physics.

引用

收藏

页数：4

相关论文

共 42 条

[1] Hybrid ab initio quantum mechanics molecular mechanics calculations of free energy surfaces for enzymatic reactions:: The nucleophilic attack in subtilisin [J].

Bentzien, J ;

Muller, RP ;

Florián, J ;

Warshel, A .

JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (12) :2293-2301

[2]

BEVERIDGE DL, 1989, COMPUTER SIMULATION, V1, P1

[3] GROUP CONTRIBUTIONS TO THE THERMODYNAMIC PROPERTIES OF NON-IONIC ORGANIC SOLUTES IN DILUTE AQUEOUS-SOLUTION [J].

CABANI, S ;

GIANNI, P ;

MOLLICA, V ;

LEPORI, L .

JOURNAL OF SOLUTION CHEMISTRY, 1981, 10 (08) :563-595

[4] THEORETICAL-EXAMINATION OF THE SN2 REACTION INVOLVING CHLORIDE-ION AND METHYL-CHLORIDE IN THE GAS-PHASE AND AQUEOUS-SOLUTION [J].

CHANDRASEKHAR, J ;

SMITH, SF ;

JORGENSEN, WL .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1985, 107 (01) :154-163

[5] A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH) [J].

Cui, Q ;

Elstner, M ;

Karplus, M .

JOURNAL OF PHYSICAL CHEMISTRY B, 2002, 106 (10) :2721-2740

[6] Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties [J].

Elstner, M ;

Porezag, D ;

Jungnickel, G ;

Elsner, J ;

Haugk, M ;

Frauenheim, T ;

Suhai, S ;

Seifert, G .

PHYSICAL REVIEW B, 1998, 58 (11) :7260-7268

[7]

Elstner M, 2000, PHYS STATUS SOLIDI B, V217, P357, DOI 10.1002/(SICI)1521-3951(200001)217:1<357::AID-PSSB357>3.0.CO

[8]

2-J

[9] A COMBINED QUANTUM-MECHANICAL AND MOLECULAR MECHANICAL POTENTIAL FOR MOLECULAR-DYNAMICS SIMULATIONS [J].

FIELD, MJ ;

BASH, PA ;

KARPLUS, M .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1990, 11 (06) :700-733

[10] Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme [J].

Hermans, J ;

Wang, L .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1997, 119 (11) :2707-2714

← 1 2 3 4 5 →