[gmx-users] g_hbond and contact

[Justin Lemkul]

On 3/4/13 11:25 AM, Kavyashree M wrote:
> Dear users,
>
> I used the following tool for finding the contacts
> g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
> -num a.xvg
>>From the index file, the number of contacts of each atom was extracted.
> This and the
> xvg output was compared with another simulation.
> It was found that the number of contacts was more in 2nd simulation
> compared to
> the first. But When I compared xvg file it was showing the opposite
> behaviour.

These statements don't make any sense.  How did you determine that the number of 
contacts in simulation 2 was greater than simulation 1, but then the .xvg files 
showed the opposite?  The number of contacts come from the .xvg files?  Perhaps 
you simply swapped your files during analysis.

> The contacts was also calculated using g_mdmat for the same cutoff and it
> was agreeing
> with the numbers I got from in index output of g_hbond.
>
> Why is this difference in index and xvg output?

An index group is a list of atom numbers.  The .xvg output is whatever you tell 
it to be, in this case, the number of contacts within the group selected.

-Justin

> Also the xvg file looks like -
>
> s0 legend "Contacts"
> @ s1 legend "Pairs within 0.4 nm"
>        4000        7496           0
>        4002        7513           0
>        4004        7605           0
>        4006        7531           0
>        4008        7573           0
>        4010        7546           0
>        4012        7544           0
>        4014        7526           0
>        4016        7530           0
>        4018        7496           0
>        4020        7526           0
> ..
>
>
> Thank you
> kavya
>

-- 
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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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