Computer simulations of a heterogeneous membrane with enhanced sampling techniques

被引:14
作者
Cherniavskyi, Yevhen K. [1 ,2 ]
Fathizadeh, Arman [3 ]
Elber, Ron [3 ,4 ]
Tieleman, D. Peter [1 ,2 ]
机构
[1] Univ Calgary, Dept Biol Sci, 2500 Dr NW, Calgary, AB T2N 1N4, Canada
[2] Univ Calgary, Ctr Mol Simulat, 2500 Dr NW, Calgary, AB T2N 1N4, Canada
[3] Univ Texas Austin, Oden Inst Computat Engn & Sci, Austin, TX 78712 USA
[4] Univ Texas Austin, Dept Chem, Austin, TX 78712 USA
基金
加拿大创新基金会; 加拿大自然科学与工程研究理事会;
关键词
MOLECULAR-DYNAMICS; LATERAL DIFFUSION; FORCE-FIELD; MODEL; LIPIDS; ORGANIZATION; NEUTRON;
D O I
10.1063/5.0014176
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
Computational determination of the equilibrium state of heterogeneous phospholipid membranes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long compared to typical time scales of computer simulations. Here, we evaluate the combination of the enhanced sampling techniques molecular dynamics with alchemical steps and Monte Carlo with molecular dynamics with a coarse-grained model of membranes (Martini) to reduce the number of steps and force evaluations that are needed to reach equilibrium. We illustrate a significant gain compared to straightforward molecular dynamics of the Martini model by factors between 3 and 10. The combination is a useful tool to enhance the study of phase separation and the formation of domains in biological membranes.
引用
收藏
页数:9
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