[gmx-users] Re: Re:Re:g_mindist option

[Tsjerk Wassenaar]

Hi Alka,

This list is not for posing riddles and puzzles, although they may be
interesting ;)
You should give all relevant information, or think carefully yourself.

Actually, it may be helpful to reformulate your riddle and let you
think about it... :p

If your cubic box has dimensions of 6 nm and you find a minimal
distance of 6 nm between a selection of atoms and its periodic images,
what does this say about the selection?

If you find a maximal internal distance within a selection of atoms of
0 nm, what does this say about the selection?

Have fun,

Tsjerk


On Wed, Aug 27, 2008 at 8:55 AM,  <alkasrivastava at iitb.ac.in> wrote:
> Thanks a lot for your reply
>
>
> Actually "maximum internal distance" is not a separate concept it is what
> i am getting in the mindist.xvg file shown below
>
> This is the mindist.xvg file:
>
>
> @  title "Minimum distance to periodic image"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Distance (nm)"
> @TYPE xy
> @ subtitle "and maximum internal distance"
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "min per."
> @ s1 legend "max int."
> @ s2 legend "box1"
> @ s3 legend "box2"
> @ s4 legend "box3"
>        0        6.000  0.000  6.000  6.000  6.000
>        0.5      6.000  0.000  6.000  6.000  6.000
>        1        6.000  0.000  6.000  6.000  6.000
>        1.5      6.000  0.000  6.000  6.000  6.000
>        2        6.000  0.000  6.000  6.000  6.000
>        2.5      6.000  0.000  6.000  6.000  6.000
>
> So according to the header information the third column (all 0.00) is the
> information for maximum internal distance but i am not getting what it
> conveys.
>
>
> Also actually may be i was not able to convey you what i wanted to ask. If
> i consider only 2D and the center one is my real box and all other are the
> periodic images. so here there are 8 periodic images 4 of them will be of
> 6nm (since my box is cubic-6nm) but 4 will be of more than 6nm (the
> diagonal one). So seeing this i am not able to justify that how could be
> the maximum distance will be 6nm.
>
>
>            :-----:-----:-----:
>            :  a  :  a  :  a  :
>            :-----:-----:-----:
>            :  a  :  a  :  a  :
>            :-----:-----:-----:
>            :  a  :  a  :  a  :
>            :-----:-----:-----:
>
> If you could please help me in this.
>
> Thanks
>
> Regards
> Alka
>
>
>
>
>
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623