Finite system and periodicity effects in free energy simulations of membrane proteins

被引：16

作者：

Bastug, Turgut ^{[1
]}

Patra, Swarna M. ^{[1
]}

Kuyucak, Serdar ^{[1
]}

机构：

[1] Univ Sydney, Sch Phys, Sydney, NSW 2006, Australia

来源：

CHEMICAL PHYSICS LETTERS | 2006年 / 425卷 / 4-6期

基金：

澳大利亚研究理事会;

关键词：

D O I：

10.1016/j.cplett.2006.05.036

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：

Periodic boundary conditions are routinely used in molecular dynamics simulations of biological systems, although they are inherently nonperiodic. Simulation artifacts that may arise from such artificial periodicity have not been well studied for membrane proteins. Here we investigate the finite size and periodicity effects in the gramicidin A peptide embedded in lipid bilayer, which offers a simple and well established test system. Comparison of free energies of translocating a potassium ion from bulk to the gramicidin A center in systems with different sizes indicate that there is no discernible effect on the free energy calculations due to finite system size and periodicity. (c) 2006 Elsevier B.V. All rights reserved.

引用

页码：320 / 323

页数：4

共 32 条

[1]

Allen M. P., 2009, Computer Simulation of Liquids

[2] Energetics of ion conduction through the gramicidin channel [J].