[gmx-users] Re: no output in g_dist

[Justin A. Lemkul]

aiswarya pawar wrote:
> Hi everyone,
> 
> when am doing this g_dist between the protein and water am getting the 
> distance between water-water. why it is so?? and is there a way i can 
> find distance in each time frame.
> 

The distance is calculated based on the groups you tell g_dist to analyze.  If 
you're getting water-water distances it's because either your index groups are 
constructed incorrectly, you're telling g_dist to do this, or you're 
misinterpreting the output.

-Justin

> Thanks
> 
> On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar <aiswarya.pawar at gmail.com 
> <mailto:aiswarya.pawar at gmail.com>> wrote:
> 
>     Hi users,
> 
>     To get the distance between water and protein i did -
> 
>      g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
> 
>     from this i should obtain an output file as distance.xvg which i
>     dont get.
> 
>     and my output is printed on the terminal as-
> 
>     t: 1  136 SOL 2336 OW  0.772373 (nm) 
>     t: 1  136 SOL 2337 HW1  0.706358 (nm)
>     t: 1  136 SOL 2338 HW2  0.807787 (nm)
>     t: 1  139 SOL 2345 OW  0.821094 (nm)
>     t: 1  139 SOL 2346 HW1  0.810919 (nm)
>     t: 1  139 SOL 2347 HW2  0.771526 (nm)
>     t: 1  7237 SOL 23640 HW1  0.997056 (nm)
>     t: 1  11793 SOL 37307 OW  0.868929 (nm)
>     t: 1  11793 SOL 37308 HW1  0.927205 (nm)
>     t: 1  11793 SOL 37309 HW2  0.776699 (nm)
>     t: 2  125 SOL 2303 OW  0.940527 (nm) 
> 
>     In this
> 
>     t: 1  136 SOL 2336 OW  0.772373 (nm) 
> 
>     does the 't' states the time frame, 136 SOL states the SOL molecule
>     number and 2336 OW the residue contact from protein and the 0.772373
>     nm the distance between them.
> 
>     Thanks
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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