GENESIS-CG-tool

This project helps you prepare topology and coordinate files for coarse-grained simulations in the MD package GENESIS.

NOTICE

From Oct 15th, 2022, the official repository of this project has been migrated to the GENESIS-release account.
This project (here) is still maintained but will contain some tools and toys of my own interests.
However, neither me nor GENESIS developers will take responsibility for the usage of these unofficial codes.

Usage

Please use the following command to show the basic usage of this tool:

./src/aa_2_cg.jl -h

A full documentation can be found from the wiki-page of this project.

Dependencies

Please run the following command to install dependencies:

./opt/dependency.jl

Tutorials

A bunch of tutorials on performing CG MD simulations with GENESIS and this project can be found from the website of GENESIS.

Branches

• The main branch is included as a part of official GENESIS release and the code only get updated when there is update in GENESIS.
• The dev branch is based on the main branch but contains newer features that will be officially released later.

Citation

If this project helps you in your research, please consider citing this publication:

• Tan C, Jung J, Kobayashi C, Torre DUL, Takada S, Sugita Y (2022) Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput Biol 18(4): e1009578. https://doi.org/10.1371/journal.pcbi.1009578