Input files for "Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field"

The performance of all-atom molecular dynamics simulations is limited by an integration time step of 2 fs, which is needed to resolve the fastest degrees of freedom in the system, namely, the vibration of bonds and angles involving hydrogen atoms. The virtual interaction sites (VIS) method replaces hydrogen atoms by massless virtual interaction sites to eliminate these degrees of freedom while keeping intact nonbonded interactions and the explicit treatment of hydrogen atoms. We have modified the existing VIS algorithm for most lipids in the popular CHARMM36 force field by increasing the hydrogen atom masses at regular intervals in the lipid acyl chains and obtained lipid properties and pore formation free energies in very good agreement with those calculated in simulations without VIS. Our modified VIS scheme enables a 5 fs time step resulting in a significant performance gain for all-atom simulations of membranes. The method has the potential to make longer time and length scales accessible in all-atom simulations of membrane–protein complexes.

The file set contains individual lipid topologies for virtual interaction sites for standard CHARMM lipids, as well as a README file with instructions on how to implement the VIS algorithm for membranes or membrane-protein complexes

Please Cite: 10.1021/acs.jctc.8b00267

全原子分子动力学模拟的性能受限于2飞秒（fs）的积分时间步长——该步长是解析体系中最快自由度所必需的，具体为涉及氢原子的键与角的振动。虚拟相互作用位点（Virtual Interaction Sites, VIS）方法通过无质量的虚拟相互作用位点替换氢原子，在保留完整非键相互作用与氢原子显式处理的同时，消除上述快速自由度。我们针对主流CHARMM36力场中的绝大多数脂质，通过在脂质酰基链中按固定间隔增大氢原子质量，对现有VIS算法进行了改进；所得脂质性质与孔形成自由能，与无VIS模拟的计算结果吻合度极佳。经改进的VIS方案可将时间步长提升至5飞秒，显著提升膜体系全原子模拟的计算性能。该方法有望实现膜-蛋白复合物全原子模拟中更长时间与空间尺度的可达性。

本数据集包含适用于标准CHARMM脂质的VIS虚拟相互作用位点专用脂质拓扑文件，以及一份README说明文档，其中详细介绍了如何在膜或膜-蛋白复合物体系中部署VIS算法。

引用格式：10.1021/acs.jctc.8b00267