Methodological issues in lipid bilayer simulations

被引:309
作者
Anézo, C
de Vries, AH
Höltje, HD
Tieleman, DP
Marrink, SJ
机构
[1] Univ Groningen, Dept Biophys Chem, NL-9747 AG Groningen, Netherlands
[2] Univ Dusseldorf, Inst Pharmaceut Chem, D-40225 Dusseldorf, Germany
[3] Univ Calgary, Dept Biol Sci, Calgary, AB T2N 1N4, Canada
关键词
D O I
10.1021/jp0348981
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
Methodological issues in molecular dynamics (MD) simulations, such as the treatment of long-range electrostatic interactions or the type of pressure coupling, have important consequences for the equilibrium properties observed. We report a series of long (up to 150 ns) MD simulations of dipalmitoylphosphatidylcholine (DPPC) bilayers in which the methodology of simulation is systematically varied. Comparisons of simulations with truncation schemes, Ewald summations, and modified Coulomb interactions, either by shift functions or reaction field models, to describe long-range electrostatics point out the artifacts inherent in each of these methods and above all those of straight cutoff methods. We further show that bilayer properties are less sensitive to the details of the pressure-coupling algorithm and that an increased integration time step of 5 fs can be safely used in simulations of phosphatidylcholine lipid bilayers.
引用
收藏
页码:9424 / 9433
页数:10
相关论文
共 55 条