Does the trajectory file need to be protein centered?

[lanselibai]

It is a common practice in Gromacs to center the protein in the .xtc file before analysing. For ProLIF, does it need to be centered as well?

I have tested raw .xtc and centered .xtc file with ProLIF, the results are similar but not exactly the same.

Which is a preferable input for ProLIF?

[cbouy]

Hi @lanselibai

Yes the trajectory needs to be centered, ProLIF calculates distances from atomic coordinates as is, there's no PBC correction applied.

[lanselibai]

thank you for clarifying it!