watterson365git / 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.

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 AmberTools20, 21 or 22.

Please see the documentation here

Cite us

Valdés-Tresanco, M.S., Valdés-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 page for more information on how to cite gmx_MMPBSA and the programs/methods implemented in it.

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Authors:

• Mario Sergio Valdés Tresanco, PhD Student. University of Medellin, Colombia
• Mario Ernesto Valdés Tresanco, PhD Student. University of Calgary, Canada.
• Pedro Alberto Valiente, PhD. University of Toronto, Canada
• Ernesto Moreno Frías, 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 principal developer) for his continuous support on ParmEd issues.
• Dr. Hymavathi Veeravarapu for helping with the introductory video for gmx_MMPBSA.
• To the Open Source license of the JetBrains programs.
• To the Sourcery team for supporting us with the Pro version.
• To all researchers that help improving gmx_MMPBSA with comments, feedback, and bug reports.

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