Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
Biochem Biophys Res Commun. 2018 Mar 29;498(2):282-287. doi: 10.1016/j.bbrc.2017.08.095. Epub 2017 Sep 7.
The determination of potentials of mean force for solute insertion in a lipid membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. Recently, a multiscale method has been proposed to leverage the conformational ensemble of a lower-resolution model as starting point for higher resolution simulations. In this work, we analyze the efficiency of this method by comparing its predictions for propanol insertion into a lipid membrane against conventional atomistic umbrella sampling simulation results. The multiscale approach is confirmed to provide accurate results with a gain of one order of magnitude in computational time. We then investigate the role of the coarse-grained representation. We find that the accuracy of the results is tightly connected to the presence of a good configurational overlap between the coarse-grained and atomistic models-a general requirement when developing multiscale simulation methods.
通过全原子分子动力学模拟确定溶质插入脂质膜的平均力势通常受到采样问题的阻碍。最近，提出了一种多尺度方法，利用低分辨率模型的构象集合作为高分辨率模拟的起点。在这项工作中，我们通过将该方法对丙醇插入脂质膜的预测与传统原子伞状采样模拟结果进行比较，来分析该方法的效率。多尺度方法被证实可以提供准确的结果，计算时间提高了一个数量级。然后，我们研究了粗粒化表示的作用。我们发现，结果的准确性与粗粒化和原子模型之间存在良好的构象重叠紧密相关-这是开发多尺度模拟方法的一般要求。
