Research data supporting 'Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy'

This file is part of the supporting data for the manuscript 'Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy', and contains scripts and code for running all-atom and coarse-grained simulations of proteins described in the manuscript.

The included README file outlines the structure of the archive and contains Lammps installation instructions for running the remaining code supplied.

There are five directories in this archive. Four of these correspond to figures in the results section of the manuscript, and each one contains a separate README file detailing its contents. They include Gromacs and Lammps scripts with example simulation set-ups to run simulations corresponding to figures 2 [potentials of mean force of all-atom models], 4 [radius of gyration simulations of coarse-grained models], 5 [direct-coexistence simulations used to determine the phase diagrams] and 6 [multiphase equilibria] of the manuscript. The directories contain input scripts and corresponding parameter and simulation configuration files, as well as example simulation output to benchmark against.

The final directory, 'all-model-parameters', contains Lammps parameter files not only for the Mpipi potential, but also for all the other models we have benchmarked in the paper. These parameter files can be used instead of the Mpipi parameters in the simulations provided in the other directories.

本文件为《基于物理驱动的近定量精度的生物分子相分离粗粒化模型》一文的辅助数据集之一，其中包含运行文中描述的蛋白质全原子和粗粒化模拟所需的脚本和代码。

所附的README文件概述了存档的结构，并包含了Lammps安装说明，以便运行提供的剩余代码。

该存档中包含五个目录。其中四个与论文结果部分的图相对应，每个目录均包含一个单独的README文件，详细说明了其内容。它们包括Gromacs和Lammps脚本，以及用于运行对应于图2（全原子模型的平均力势）、图4（粗粒化模型的回转半径模拟）、图5（用于确定相图的直接共存模拟）和图6（多相平衡）的示例模拟设置。

目录中包含输入脚本以及相应的参数和模拟配置文件，以及用于基准测试的示例模拟输出。

最后一个目录‘all-model-parameters’包含的Lammps参数文件不仅包括Mpipi势能，还包括我们在论文中基准测试的所有其他模型。这些参数文件可以在其他目录提供的模拟中替代Mpipi参数使用。