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
lowlearner is a code for learning collective variables (CVs) from standard
and enhanced sampling simulations. Installation script and examples can
be found in the Zenodo dataset. It is
implemented as a module for PLUMED2,
an engine for free energy calculations of atomistic systems and enhanced
sampling. The code requires PLUMED to be linked with LibTorch v1.8.
To use the module, you need enable lowlearner by adding the
--enable-modules=lowlearner or --enable-modules=all
to the PLUMED configure command. You can follow the instructions given
here.
For example:
> ./configure --enable-modules=lowlearner
> make -j 4
> make install
You can ask questions or join the development discussion on PLUMED Google group.
maze
maze is a code that implements enhanced sampling methods for sampling the
reaction pathways of ligand unbinding. It can be installed as a module in
PLUMED similarly to the lowlearner module.
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.
References
-
J. Rydzewski, and O. Valsson
Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling
J. Phys. Chem. A 125, 6286 (2021)
doi:10.1021/acs.jpca.1c02869 / arXiv:2007.06377 / Zenodo:4756093 / plumID:21.023 -
J. Rydzewski, M. Chen, T. K. Ghosh, O. Valsson
Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
J. Chem. Theory Comput. 18, 7179 (2022)
doi:10.1021/acs.jctc.2c00873 / arXiv:2207.14554 / plumID:21.023 -
J. Rydzewski
maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
Comp. Phys. Commun. 247, 106865 (2020)
doi:10.1016/j.cpc.2019.106865 / arXiv:1904.03929 / plumID:19.056 -
J. Rydzewski, and O. Valsson
Finding Multiple Reaction Pathways of Ligand Unbinding
J. Chem. Phys. 150, 221101 (2019)
doi:10.1063/1.5108638 / arXiv:1808.08089 / plumID:19.066