.xtc file for calculations

[Janus Quiambao]

Good day!

I am currently trying to calculate the binding energy of my protein-protein system and was wondering about the type of .xtc file needed. This is because in analyzing the rmsd, rmsf of my system, I applied PBC correction to my original trajectory. I would like to ask if the .xtc file should be the one that is not corrected i.e., the .xtc file that contains the original trajectory, or the PBC corrected one? Will choosing one over the other have some kind of effect to the calculations?

Thank you in advance!

[marioe911116]

You should use the .xtc with PBC correction

[Janus Quiambao]

I see. Thank you!

Follow-up question, I want to analyze interaction entropy in my system and for the binding free energy calculations, I want to compare Single Trajectory and NLPB. Do I do this in two separate files, or can I do both calculations in 1 input file, but separated

/

&gb

/

&pb

/

like this?

Thank you again!

[marioe911116]

Technically, you could run both in the same run, although I'll suggest run them separately for better clarity in the results files

[jiquiambao]

Thank you!