maize-biosimspace#
maize is a graph-based workflow manager for computational chemistry pipelines. This repository contains a namespace package providing BioSimSpace extensions for maize. You can find the core maize documentation here.
Quick Start#
Clone the repository and install:
git clone https://github.com/fjclark/maize-biosimspace.git
cd maize-biosimspace
mamba env create -f env-users.yml
mamba activate maize-biosimspace
pip install --no-deps ./
Ensure that the required AMBER, GROMACS, and NAMD executables are available in your environment if you plan to use the relevant nodes.
Many maize-biosimspace workflows will now be available through CLIs. Try typing bss_ and hitting tab to list them. To see the options for each, type e.g.
bss_parameterise -h
To run production 0.1 ns of production MD on a protein-ligand complex using GROMACS, dumping all of the intermediate files to the current directory:
mkdir gmx_md_example
cd gmx_md_example
cp ../tests/data/complex.* .
bss_production_gromacs --inp complex.prm7 complex.rst7 --runtime 0.1 --save_name gmx_md_out --dump_to .
This will run locally. To configure maize nodes to run through a scheduler such as slurm, see Configuration.