[gmx-users] different g_hbond result for two run

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 3 12:13:00 CEST 2008

vivek sharma wrote:
> hi all,
> I was trying to analyze some h_bond interaction for a protein with one 
> ligand. I tried two runs for the same one for 5 nsec and another for 10 
> nsec.
> What I found here is that, the h-bonds present in the 5 nsec trajectory 
> are more than that in 10 nsec trajectory, h-bonds in 10 nsec run should 
> be at least equal to that in 5 nsec run.

g_hbond measures the number of H-bonds per timeframe.  What makes you think that 
the 10-ns trajectory should have more H-bonds than the 5-ns trajectory?  Maybe 
some H-bonds are formed, then broken.

> for the two trajectory i have taken out the 10 frames. are the 
> interaction picked up by g_hbond are dependent on the full trajectory or 
> the frames only.
> whether the two different run on the same input file with same parameter 
> can be related or compared ?

g_hbond is only dependent upon individual frames; there are not fits or 
progressive information to be stored.  The input file (.tpr) is read in to get 
the atom types that g_hbond uses to determine H-bond donors and acceptors.

> Can anybody help me in the same case by giving some explanation or 
> giving right way to do it ?

You haven't done anything wrong, you just may need to adjust your interpretation 
of the output :)


> With Thanks,
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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