Confusion regarding the trajectory file to be used

[Prabuddha Bhattacharya]

Hello Community

I am new to the group and a beginner in the field of MD Simulation and MMPBSA calculation. I am having a confusion regarding the trajectory file to be used for the MMPBSA/GBSA calculation.

For a protein-ligand complex, is it fine if I only make the PBC corrections with the trajectory file (.xtc) and use this PBC corrected xtc file for the subsequent calculations using the -ct flag? I have done this and had an errorless calculation. The command that I ran was as follows: gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct system.xtc -lm ligand.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv (here the "system.xtc" implies the final MD output trajectory for the total system with only the PBC corrections)

Or do I also need to remove the solvent and ions from the trajectory file along with making the PBC corrections? Is my earlier approach of retaining the water and ions in the trajectory leading to inaccurate results?

I will be extremely grateful if somebody helps me to clarify my doubts.

Thank you and best regards.

Prabuddha Bhattacharya

[Mario Ernesto]

You can remove the solvent and ions, and work with that trajectory... :)

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[Prabuddha Bhattacharya]

Dear Sir

Thank you so much for your kind response. 

So in case I retain the water and ions in the trajectory file and only make the PBC corrections, the MMPBSA results obtained from that xtc file would be inaccurate? 

Or this removal of solvent and ions from the xtc is to just reduce the required computational resources? 

Will there be any difference in the results obtained from both these approaches? If so, then which one is expected to be more accurate/realistic?

Thank you in advance.

Best regards 

[Mario Ernesto]

gmx_MMPBSA removes the water and ions during the preparation step as it's not needed for the calculations... In case you remove the water and ions by yourself, you can specify the solvated_trajectory=0 in the &general namelist, so that way gmx_MMPBSA skip this step and save some time :)

[Prabuddha Bhattacharya]

Thank you so much sir for the clarification.

Best regards

Prabuddha Bhattacharya