Software
MAZE
Module for PLUMED2
Information
maze
(version 1.0)
Heterogeneous Ligand Unbinding along Transient Protein Tunnels
Github
Page
arXiv
MAZE
is a code that implements enhanced sampling methods for sampling the
reaction pathways of ligand unbinding. It is made as a module for
PLUMED2, an engine for
free energy calculations of atomistic systems and enhanced sampling.
Download and Install
You need to download the MAZE
repository and enable the MAZE
module by adding
the --enable-modules=maze
to the PLUMED configure command. You can follow the
instructions given
here.
For example:
> ./configure --prefix=/usr/local --enable-modules=maze
> make -j 4
> make install
Author
The MAZE
module is developed and maintained by Jakub Rydzewski (Nicolaus
Copernicus University), jr@fizyka.umk.pl.
Support
You can ask questions or join the development discussion on:
- the Gitter channel.
- the PLUMED Google group.
You can also post bug reports and feature requests in Github issues. Make sure to read the Plumed guidelines first.
Citation
If you find this useful, please cite the methods which MAZE
is based on
using:
@article{rydzewski2019finding,
title={Finding Multiple Reaction Pathways of Ligand Unbinding},
author={Rydzewski, Jakub and Valsson, Omar},
journal={J. Chem. Phys.},
volume={150},
pages={221101},
year={2019}
}
and
@article{rydzewski2019maze,
title={maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels},
author={Rydzewski, Jakub},
journal={Comp. Phys. Commun.},
pages={106865},
volume={TBA},
year={2019}
}
Funding
During its development, MAZE
was funded by the National Science Center grants
no. 2015/19/N/ST3/02171, 2016/20/T/ST3/00488, and in part by 2016/23/B/ST4/01770.