Microcanonical replica exchange molecular dynamics simulation of proteins

被引：16

作者：

Kar, Parimal ^{[1
]}

Nadler, Walter ^{[2
]}

Hansmann, Ulrich H. E. ^{[1
]}

机构：

[1] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA

[2] KFA Julich GmbH, Forschungszentrum, IAS, JSC, D-52425 Julich, Germany

来源：

PHYSICAL REVIEW E | 2009年 / 80卷 / 05期

基金：

美国国家科学基金会;

关键词：

molecular biophysics; molecular dynamics method; proteins; FORCE-FIELD; MONTE-CARLO; CAGE; SOLVATION;

D O I：

10.1103/PhysRevE.80.056703

中图分类号：

O35 [流体力学]; O53 [等离子体物理学];

学科分类号：

070204 ; 080103 ; 080704 ;

摘要：

We present microcanonical replica exchange molecular dynamics simulations as an alternative to canonical ones. Its advantage is the easily tunable high acceptance rate for replica exchange. We present the theory, comment on its actual implementation, and demonstrate its application for a common test case, the trp-cage protein.

引用

页数：8

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