Time duration and input file editing

[Aswin Mohan]

Hi there,

Am new to MM PBSA calculation. I had completed MD simulation of protein-ligand system using charmmff and gromacs 2020.6. I wish to calculate MM PBSA using gmx_MMPBSA tool. I had generated the input file using gmx_MMPBSA --create_input pb command. I had edited the input file at the atart frame and end frame and changed the PBRadii to 7.

1) Do I have to change anymore parameters in the input file?

2) May I know an approximate time duration to complete 200 frames MM PBSA calculation(as mentioned in the attched file) in a system with the following specifications.

Memory: 7.6 GiB

Processor: 11th Gen Intel® Core™ i5-1135G7 @ 2.40GHz × 8

Graphics: Mesa Intel® Xe Graphics (TGL GT2)

[marioe911116]

The duration of the PB calculations depends on the number of atoms, frames, and hardware properties... For you to have an idea, a system of 608 atoms (this is excluding solvent and ions, just the complex), 10 frames on my computer (AMD Ryzen 7 2700X Eight-Core Processor × 8, 32GB RAM) take approximately 1 minute and a half... in your case, I will recommend to run the calculation with one frame and see how long it takes, then multiply that by 200 and you will have a fair estimate of the time required for the calculation. Careful when using multiprocessing on your machine as I see that you only have 8GB RAM and PB calculation can be pretty consuming...

hope this helps!

[Mario Ernesto]

There are no differences in &pb parameters between the two input files... just differences in format... the one in the tutorials has a format more similar to Amber's while the one you generated with --create command is more similar to GROMACS format...

more info on the input file here (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/input_file/)

hope this helps!

El vie, 3 jun 2022 a las 13:09, 'Aswin Mohan' via gmx_MMPBSA (<gmx_m...@googlegroups.com>) escribió:

may I know the difference in results between the mmpbsa.in file provided in the protein-ligand charmff folder(got this folder while running the gmx_MMPBSA_test) and the input file I had attached earlier?

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[Aswin Mohan]

Thank you for making this clear Mario.