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Cheng Tan edited this page Oct 14, 2022 · 7 revisions

Welcome to the genesis_cg_tools wiki!

The project is to help you prepare molecular dynamics (MD) files for running coarse-grained (CG) simulations with the software GENESIS.

The main entrance of the project is genesis_cg_tools/src/aa_2_cg.jl. Here we introduce the common usage of this tool and explain the command line arguments.

Installation

The project is hosted on Github (https://github.com/genesis-release-r-ccs/genesis_cg_tool) and included as a part of GENESIS (>1.7). You can download the code of GENESIS-cg-tool from here or from the download page of GENESIS.

Dependencies

The main programming language of this project is julia. Therefore, you have to first download and install julia. You also have to install some dependencies by running genesis_cg_tools/opt/dependency.jl.

Basic Usage

Help

To get help from the command line: genesis_cg_tools/src/aa_2_cg.jl -h. This command prints out the basic usage information and a full list of arguments.

Information Flow

Basically, the program reads experimental data (usually structural information) to generate the CG topology and coordinate files that GENESIS can understand.

Get Started

As the simplest example, assume that we have an all-(heavy)-atom PDB file for a protein, prot.pdb, and run the following command:

genesis_cg_tools/src/aa_2_cg.jl prot.pdb

this will generate three files:

  • prot_cg.gro: the structure file that contains the coordinates of the CG particles;
  • prot_cg.top: the topology file that contains molecule information;
  • prot_cg.itp: the topology file that contains detailed atom and interaction information.

These files are in the Gromacs format with some options specific for GENESIS. You can find a detailed description of the structure of these File Formats.

Arguments

aa_2_cg.jl accepts arguments from either the command-line or a toml-format configuration file. For example, with the "-v" (or "--verbose") option, more information will be printed to the standard output. Here is a detailed description of Command Line Arguments.