Input files for setup and running metadynamics simulations for ligand dissociation
These are input files for running a sample simulation for running metadynamics for simulations of ligand dissociation from a protein. The files are set up for use with GROMACS 5.1 and may be incredibly outdated.
These will hopefully serve as a reference for any inspiration one should need for collective variables though!
If you do use these files, or find them helpful, please cite the following paper:
Sukrit Singh, Xianqiang Sun, Kendall J Blumer, Gregory R Bowman (2018) Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding eLife 7:e38465.
Bibtex:
@article {10.7554/eLife.38465,
article_type = {journal},
title = {Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding},
author = {Singh, Sukrit and Sun, Xianqiang and Blumer, Kendall J and Bowman, Gregory R},
volume = 7,
year = 2018,
month = {oct},
pub_date = {2018-10-05},
pages = {e38465},
citation = {eLife 2018;7:e38465},
doi = {10.7554/eLife.38465},
url = {https://doi.org/10.7554/eLife.38465},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}
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