[gmx-users] how to use the triplets index file generated by g_hbond

[Justin A. Lemkul]

The first entry in summary_HBmap.dat is index zero (i.e., the "bottom" of the 
plot area).  So the results look fine to me.

-Justin

On 5/14/12 1:02 PM, Yun Shi wrote:
> Hi Justin,
>
> Thank you for the perl script. But I wonder now why there is a difference
> between what shows in the hbmap.xpm file and the summary_HBmap.dat generated.
>
> For example, I found many occurrences of the second to last H-bond in the
> 20hbmap.xpm file attached (visualized by GIMP), but in the summary_HBmap.dat
> file there showed only 0.1 % Exist. of this specific H-bond.
>
> Anything wrong with my interpretation?
>
> Please see attached the files I used/ generated.
>
> Thanks,
> Yun
>
>
>
> On Sat, May 5, 2012 at 10:43 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 5/5/12 1:22 PM, Yun Shi wrote:
>
>         Hello all,
>
>         I have used g_hbond with -hbn option to generate a .ndx file that has
>         Acceptor -
>         Donor - Hydrogen in each line of the last index group.
>
>         But I wonder I could I use this index file to monitor each hydrogen bond
>         specified by these triplets along the trajectory?
>
>
>     Depending on what you're trying to do, you can map the triplets in hbond.ndx
>     with the hbmap.xpm file to obtain, for instance, the % of total frames that
>     a particular hydrogen bond exists.  I've done something along those lines
>     with a script I call plot_hbmap.pl <http://plot_hbmap.pl>, available from:
>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__scripts.html
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html>
>
>     Please note the usage information in the header of the file.
>
>
>         Also, I understand that the -ins in no longer available. But how can we
>         analyze
>         those water-mediated hydrogen bonds?
>
>
>     Doing something like this will require careful use of index groups and
>     external scripting.  Presumably, if you have two groups (let's call them A
>     and B), if group A forms hydrogen bonds to a certain group of SOL residues,
>     and if group B does the same, with some of those SOL molecules overlapping
>     in some given frames, you can make an argument for a water-mediated hydrogen
>     bond. Determining the existence of the hydrogen bonds is easy with g_hbond
>     and index groups.  Determining simultaneous occurrence requires an external
>     script, and can make use of hbmap.xpm (to determine which frames contain the
>     hydrogen bonds) and hbond.ndx (to determine which groups are participating
>     in those hydrogen bonds).
>
>     -Justin
>
>     --
>     ==============================__==========
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
>     ==============================__==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
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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