[gmx-users] Re: no output in g_dist

[aiswarya pawar]

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.

Thanks

On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar <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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