Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
The Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
J Chem Phys. 2020 Oct 14;153(14):144110. doi: 10.1063/5.0014176.
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.
计算确定异质磷脂膜的平衡状态是一项重大挑战。我们希望探索这些多组分系统的丰富相图。然而,与计算机模拟的典型时间尺度相比,膜中的扩散和混合时间很长。在这里,我们评估了增强采样技术分子动力学与化学计量学步骤以及蒙特卡罗与粗粒度膜模型(Martini)的分子动力学的组合,以减少达到平衡所需的步骤和力评估的数量。与 Martini 模型的直接分子动力学相比,我们通过 3 到 10 倍的因子说明了显著的增益。该组合是增强生物膜相分离和域形成研究的有用工具。