https://github.com/ale94mleon/gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

https://github.com/ale94mleon/gmx_mmpbsa

Repository

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

https://github.com/ale94mleon/gmx_MMPBSA/blob/master/

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# Welcome to gmx_MMPBSA!
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS 
files. It works with all GROMACS versions along with AmberTools >= 20.

**Please see the documentation [here](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/getting-started)**

## Cite us



Valds-Tresanco, M.S., Valds-Tresanco, M.E., Valiente, P.A. and Moreno E. **gmx_MMPBSA: A New Tool to Perform 
End-State Free Energy Calculations with GROMACS**. _Journal of Chemical Theory and Computation_, 2021 17 (10), 6281-6291
https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645

Please also consider citing MMPBSA.py's paper:

Bill R. Miller, T. Dwight McGee, Jason M. Swails, Nadine Homeyer, Holger Gohlke, and Adrian E. Roitberg. **MMPBSA.py: 
An Efficient Program for End-State Free Energy Calculations**. _Journal of Chemical Theory and Computation_, 2012 8 
(9), 3314-3321. https://pubs.acs.org/doi/10.1021/ct300418h

Please, visit [Cite gmx_MMPBSA](cite_us.md) page for more information on how to cite gmx_MMPBSA and the programs/methods implemented in it.

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Authors:
- [Mario Sergio Valds Tresanco](https://www.researchgate.net/profile/Mario-Valdes-Tresanco-2), PhD Student. _University of Medellin, Colombia_
- [Mario Ernesto Valds Tresanco](https://www.researchgate.net/profile/Mario-Valdes-Tresanco), PhD Student. _University of Calgary, Canada._
- [Pedro Alberto Valiente](https://www.researchgate.net/profile/Pedro-Valiente), PhD. _University of Toronto, Canada_
- [Ernesto Moreno Fras](https://www.researchgate.net/profile/Ernesto-Moreno-Frias), PhD. _University of Medellin, Colombia_

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Acknowledgements:
- First of all, to Amber and GROMACS developers. Without their incredible and hard work, gmx_MMPBSA would not exist.
- Jason Swails (Amber developer and [ParmEd](https://github.com/ParmEd/ParmEd) principal developer) for his continuous support on ParmEd issues.
- Dr. Hymavathi Veeravarapu for helping with the [introductory video](https://www.youtube.com/watch?v=_2mYeffqFIo) for gmx_MMPBSA.
- To the Open Source license of the [JetBrains](https://www.jetbrains.com) programs.
- To the [Sourcery](https://sourcery.ai/invite/gndRrjlo) team for supporting us with the [Pro version](https://sourcery.ai/pro/).
- To all researchers that help improving gmx_MMPBSA with comments, feedback, and bug reports.

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