Software
- PLUMED – an open-source, community-developed library that provides methods for enhanced sampling, free energy estimation, and analysis of molecular dynamics (MD) simulations.
Modules for PLUMED2:
lowlearner
maze
maze (version 1.0) [1,2]
Github
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.
To use the module, you need enable maze by adding the --enable-modules=maze
to the PLUMED configure command. You can follow the instructions given
here.
For example:
> ./configure --enable-modules=maze
> make -j 4
> make install
You can ask questions or join the development discussion on PLUMED Google group.
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.
-
J. Rydzewski
maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
Comp. Phys. Commun. 247, 106865 (2020)
DOI arXiv plumID:19.056 -
J. Rydzewski, and O. Valsson
Finding Multiple Reaction Pathways of Ligand Unbinding
J. Chem. Phys. 150, 221101 (2019)
DOI arXiv plumID:19.066