[gmx-users] RE: g_mindist option

van Bemmelen J.J.M.vanBemmelen at student.TUDelft.NL
Wed Aug 27 17:10:14 CEST 2008

Hi Alka,

>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.

>From the manual of g_mindist
"It also plots the maximum distance within the group". Since your group
consists of only one atom (the c-alpha), the maximum distance WITHIN the
group is 0 nm.

>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.

I see what you mean. I agree with you that the -max option does not seem
to work as expected (i.e. "Calculate *maximum* distance instead of
minimum". BETWEEN groups I assume, since it doesn't say otherwise), or
that it simply doesn't seem to work at all with the option -pi enabled.

However, I'm not a developer nor an expert on g_mindist, so I can't
really help you with this. Maybe you can try to look into the source
code yourself to see what is going on. :-)

By the way, which version of GROMACS are you using? Maybe this was
already reported and has already been changed for newer versions. You
could check bugzilla, but that option seems to be broken at the moment
(You don't have permission to access the requested directory), at least
not on my machine.


More information about the gromacs.org_gmx-users mailing list