[gmx-users] Possible problem with g_hbond

[Justin Lemkul]

On 7/16/12 10:59 AM, Andrew DeYoung wrote:
> Hi,
>
> If you have time, I'm wondering if you can please help me to think through a
> problem that I seem to be having with g_hbond.  I am looking for a way to
> list the _individual_ hydrogen bonds as a function of time, by indices --
> more than just determining the number of hydrogen bonds at every timestep.
> So, at every timestep, I would like to somehow list the hydrogen bonds that
> exist during that time.  At timestep 1, for example, a hydrogen bond might
> exist between oxygen26 and hydrogen353.  But at timestep 2, this same
> hydrogen bond may no longer exist because oxygen26 and hydrogen353 have
> drifted beyond the cutoff.  At timestep 3, the hydrogen bond may exist again
> because the atoms have drifted together.
>
> Do you know if generating such a list is possible, perhaps with g_hbond?
>
> I was thinking that perhaps such information would be listed in the log
> file, which, according to the manual, is output using the -g flag.  So, I
> have tried the following command in g_hbond_d (I had run double precision
> simulations):
>
> g_hbond_d -f traj.trr -s topol.tpr -n index.ndx -g test.log
>
> (I select two non-overlapping groups in index.ndx when prompted.)  I also
> tried the same without "_d":
>
> g_hbond -f traj.trr -s topol.tpr -n index.ndx -g test.log
>
> But in both cases, I do not obtain test.log or any log file; I only obtain
> hbnum.xvg from the -num flag, which is non-optional output.
>
> Have you ever experienced the -g flag apparently not working in g_hbond?  Do
> you have any thoughts about what I can try differently?  Thanks!
>

The output you want is contained in the .xpm file produced with the -hbm flag, 
and the hydrogen bonds are listed in the index file produced by -hbn.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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