How to calculate enthalpy (dH) and entropy (IE) on the different periods of frames without using GUI (gmx_MMPBSA_ana)

[Mark Chen]

Dear Sir,

I would like to ask how to calculate enthalpy (dH) and entropy (IE) on the different periods of frames without using GUI (gmx_MMPBSA_ana).

I had already calculated antigen-antibody complexes using MD simulation.

MD simulations : GROMACS 2025.1, 100ns, TIP3P, CharMM36m FF;

gmx_MMPBSA: Start frame 5001, end frame 10001;

I would like to analyze the dH and -TdS on the period of frames, as below:

start: 5001, end 10001

start: 6001, end 10001

start 7001, end 10001

How can I do the calculation without using GUI ?

Sincerely

Thank you

Mark

[mariosergi...@gmail.com]

Although you could use the Python API, I certainly don't recommend it because we don't have it documented...
Why don't you use gmx_MMPBSA_ana? Note that you can copy the files to your PC and run them there...

[mariosergi...@gmail.com]

Oh, I see... Please send me the file folder (don't include the MD files, just the calculation files) so I can reproduce the problem. I'll try to make a script for you so you can make these changes via scripting.

[mariosergi...@gmail.com]

I attached a script to extract the data you need.

Notes:
- There was a small bug in the activation of the IE calculation in the API. If only the ie_segment changes, the IE was not recalculated. And if the number of frames was changed, but the value ie_segment=25 was set, and it had been defined differently in the input file, the SD was not calculated either. This was fixed in the master branch on GitHub. Please update the app using the development version.
- There are several issues related to your calculations, not the app.
1. You defined the IE calculation interval as 100%; this is not recommended due to the nature of the IE calculation. It is recommended to use an interval within which the curve has stabilized. However, if you are not satisfied with the result, you can change it in gmx_MMPBSA_ana or the script.
2. Based on your trajectory info, you use 10ps as the interval, but the recommended interval is 0.1ps. Please, check the documentation
3. I don't know if you checked that there's a WARNING in your output file indicating that the IE is unreliable due to the sigma value you obtained. Please, check the documentation
4. DH ~= -18 kcal. For such a large system, I would expect something larger, but this certainly depends on the system. But I would check because the energy tends to increase. This is evident in the fact that the SD value is almost comparable to the value you obtain.
5. IMHO, I would desist from using IE since it involves running MDs with very rigid conditions and a very small interval, and I would concentrate on the analysis at the DH level. For Ag-Ab, I would use decomposition, which gives a view somewhat more focused on mutations rather than using global metrics.

As for the script, it's quite intuitive. Simply change wdir to your folder with the same structure you sent me and any parameters you need. This will generate a CSV file with all the information. This script must be executed in the gmxMMPBSA environment