Supporting data for transmembrane domain self association simulations in "Recalibration of protein interactions in Martini 3"

This repository contains the data of transmembrane helix self-association simulation from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, along with two modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor λPW, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor λPP. The simulation files are kept in one single zip file, which contains trajectories for two protein EphA1 and ErbB1 systems with three versions of force fields. The trajectory files are in xtc format, and are accompanied by a structure in pdb format for system topology and a tpr file to start the simulation. In each version of force field for each protein, name of the files corresponds to that specific umbrella sampling window. Umbrella sampling windows ranges from 0.6 nm to 3.4 nm with a spacing of 0.2 nm.

本仓库收录了来自《Martini 3中蛋白质相互作用的重新校准》一文的跨膜螺旋自缔合模拟数据。本次模拟采用Martini 3.0力场运行，同时包含两个Martini 3.0修改版本：其一将所有蛋白质珠子与水珠子间的伦纳德-琼斯（Lennard-Jones）势阱深度ε通过因子λPW进行缩放，其二将所有蛋白质珠子间的伦纳德-琼斯势阱深度ε通过因子λPP进行缩放。所有模拟文件打包于单个zip压缩包中，包含EphA1与ErbB1两种蛋白质体系在三种力场版本下的模拟轨迹。轨迹文件格式为xtc，配套有用于体系拓扑定义的pdb格式结构文件，以及用于启动模拟的tpr文件。针对每种蛋白质的每种力场版本，文件名与其对应的特定伞形采样窗口一一对应。伞形采样窗口的取值范围为0.6 nm至3.4 nm，步长为0.2 nm。