On Thu, Sep 8, 2011 at 8:25 PM, aiswarya pawar <aiswarya.pa...@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.
The -dist option: Print all atoms in group 2 (water) closer than dist to
the center of mass of group 1 (protein in
your case).
As you have seen, it *print* the result on the screen.
To obtain the distance.xvg file, please don't use the -dist option here.
>
> 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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--
Best Regards,
lina
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