[gmx-users] g_dist error

[Justin A. Lemkul]

aiswarya pawar wrote:
> Hi Justin,
> 
> Am using g_dist to find the distance between water and protein. for that i made a index file such as-
> 
> a CA(protein atoms)
> 
> a OW(water atoms)
> 
> i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
> 
> 
> 
> instead of getting the result for protein-SOL distance . my output shows SOL-OW distance as seen below-
> 
> t: 1  136 SOL 2336 OW  0.772373 (nm)
>  
> even after specifying am getting an wrong output.
> 

I don't know why this shows up if you're using "-dist 0.35" but it still sounds 
like you're going about your task the wrong way.  If you want the distance 
between CA atoms and water as a function of time, leave off -dist and the output 
you want is in the dist.xvg file written by g_dist (-o output option).  This 
will be a relatively insensitive measurement and you will probably need better 
index groups.

-Justin

> 
> Thanks
> 
> 
> 
> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     aiswarya pawar wrote:
> 
>         Hi Users,
> 
>         Am using g_dist to find the distance between water and protein.
>         but my output has the values of SOL-water distance.
> 
>         t: 1  136 SOL 2336 OW  0.772373 (nm)
> 
> 
>     This is not a water-water distance, it is the output of the -dist
>     option telling you that water molecule 136 has its OW atom at
>     0.7723273 nm from whatever your reference group is.
> 
>     -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
>     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. 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

========================================