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.