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

Citation

Joseph, J., Reinhardt, A., Aguirre, A., Chew, P. Y., Russell, K., Rene Espinosa, J., Garaizar, A., & et al. (2021). Research data supporting ‘Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy’ [Dataset]. www.repository.cam.ac.uk/handle/1810/329039

Description

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.

Format

Lammps, 10Mar2021; Gromacs 4.5

Keywords

coarse-grained modelling, liquid-liquid phase separation

Rights

Attribution 4.0 International

Read more here: Source link