[gmx-users] Gmx hbond

[rose rahmani]

Hi,

I have 2 questions, but please consider them 2 distinct questions and are
not related.
I did umbrella sapmling and calculate the PMF.
Now i I want to calculate number of hydrogen bonds for amino acid in its
initial distance(far from surface) and binding distance ( which is close to
surface and PMF is minimum there).
1- Is it rational to use pulling data(traj.xtc, .tpr,...) to calculate this
analysis, as it is nonequilibrium condition?
2- Is it better to choose initial frame and binding frame, do umbrella
sampling step (, nvt) and calculate number of hbons separately and compare
the result? Is it true to compare them in this condition?

With regards
Rose