# gmx\_MMPPBSA analysis

**URL:** https://gromacs.bioexcel.eu/t/gmx-mmppbsa-analysis/8131
**Category:** User discussions
**Created:** [January 24, 2024, 8:59pm UTC](https://gromacs.bioexcel.eu/t/gmx-mmppbsa-analysis/8131 "2024-01-24T20:59:15Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![jishrat17](https://avatars.discourse-cdn.com/v4/letter/j/a698b9/32.png) [@jishrat17](https://gromacs.bioexcel.eu/u/jishrat17)
#### Post date: [January 24, 2024, 8:59pm UTC](https://gromacs.bioexcel.eu/t/gmx-mmppbsa-analysis/8131/1 "2024-01-24T20:59:15Z")

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GROMACS version: 2023  
GROMACS modification: Yes/No  
Hi everyone,  
I have done the MD simulation of the protein-peptide system using the charmm36 force field. After that, I tried calculating the binding free energy between protein and peptide using gmx\_MMPBSA and plotted the graph between delta G and frame #. In the plot, the value of delta G is 0 at some frame. What does that indicate? I have applied the PBC on the trajectory but still getting the same results.  
Any comments or suggestions regarding this will be highly appreciated.  
I really appreciate any help you can provide.

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### Author: ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)
#### Post date: [January 25, 2024, 8:02am UTC](https://gromacs.bioexcel.eu/t/gmx-mmppbsa-analysis/8131/2 "2024-01-25T08:02:24Z")

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As I just replied in another thread, [G\_mmpbsa analysis - #2 by MagnusL](https://gromacs.bioexcel.eu/t/g-mmpbsa-analysis/8125/2), there are not many gmx\_mmpbsa experts here.

I haven’t used the gmx\_mmpbsa tool at all myself, but in general, when you analyse `delta G` you always need to know what you are comparing to. If not having a specific reference state, it is common to set the lowest `delta G` to 0. You could then consider `delta G` to be `delta delta G` relative to the most favourable configuration. However, if many frames have exactly `delta G` 0, that is suspicious.

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### Author: ![Ishrat](https://avatars.discourse-cdn.com/v4/letter/i/ec9cab/32.png) [@Ishrat](https://gromacs.bioexcel.eu/u/Ishrat)
#### Post date: [January 25, 2024, 7:44pm UTC](https://gromacs.bioexcel.eu/t/gmx-mmppbsa-analysis/8131/3 "2024-01-25T19:44:03Z")

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Thank you for the reply.  
I have used starting structure as a reference, so if delta G is zero it means w.r.t reference there is no difference is binding at that particular frame.