[gmx-users] g_mindist doubt

[aiswarya pawar]

Hi Tsjerk,

i used the command in format-

g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b
500 -e 1500 -d 0.5

so here i obtain the output-

atmpair.out-

0.000000e+00            13         21161
1.000000e+00            13         21161
2.000000e+00            13         21161
3.000000e+00            13         21161
4.000000e+00            13         21161
5.000000e+00            13         21161
6.000000e+00            13         21161
7.000000e+00            13         21161
8.000000e+00            13         21161
9.000000e+00            13         21161
1.000000e+01            13         21161
1.100000e+01            13         21161
1.200000e+01            13         21161
1.300000e+01            13         21161
1.400000e+01            13         21161
1.500000e+01            13         18698
1.600000e+01            13         21161
1.700000e+01            13         18698
1.800000e+01            13         18698
1.900000e+01            13         18698
2.000000e+01            13         18698
2.100000e+01            13         21455
2.200000e+01            13          7142
2.300000e+01            13          7142


and distance output-

0.000000e+00  1.360443e+00
1.000000e+00  1.246777e+00
2.000000e+00  1.386871e+00
3.000000e+00  1.250959e+00
4.000000e+00  1.314306e+00
5.000000e+00  1.273990e+00
6.000000e+00  1.175991e+00
7.000000e+00  1.154678e+00
8.000000e+00  1.249905e+00
9.000000e+00  1.110049e+00
1.000000e+01  1.023204e+00
1.100000e+01  1.004968e+00
1.200000e+01  1.214452e+00
1.300000e+01  1.297469e+00
1.400000e+01  1.307791e+00
1.500000e+01  1.276168e+00
1.600000e+01  1.552775e+00
1.700000e+01  1.668275e+00
1.800000e+01  1.786125e+00
1.900000e+01  1.733398e+00
2.000000e+01  1.656987e+00
2.100000e+01  1.715875e+00
2.200000e+01  1.848419e+00
2.300000e+01  1.932844e+00


Now my doubt is the whether these distances shown are the exact distance ie
actual or the minimum distance measured between the two atoms.

Thanks

On Thu, Sep 22, 2011 at 12:13 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi Aiswarya,
>
> What did you do, what did you get, what did you expect and what is
> your hunch regarding the difference between your result and your
> expectation?
>
> Tsjerk
>
> On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
> <aiswarya.pawar at gmail.com> wrote:
> > Hi users,
> >
> > The g_mindist gives the minimum distance between the atoms other than the
> > actual distance.
> >
> > Thanks
> >
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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