[gmx-users] Re:g_mindist option

[Justin A. Lemkul]

alkasrivastava at iitb.ac.in wrote:
> Hi
> 
> I am doing a 5 peptide simulation in a 6nm box. Now to check the
> correctness of my simulation i m calculating the minimum periodic distance
> using g_mindist to find out the distance between molecule and its periodic
> images.Following is the command i have used
> 
> g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg
> 
> For the selection criteria i have used c-alpha atom of peptide 1. It is
> giving me the minimum distance of 6nm as expected but how can i see the
> maximum distance because by applying -max option also i am getting the
> same result
> 
> 

The result should be the same.  Think about what PBC does.  It puts an identical 
image of your system all the way around, so every move your solute makes is 
equally represented in all directions.  The distance between periodic images 
will be the same, whether you look at the maximum distance or the minimum distance.

> 
> 1. g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg
> 
> Select a group: 19
> Selected 19: 'c-alpha-gly1'
> Reading frame   16600 time 8300.000
> 
> The shortest periodic distance is 6 (nm) at time 0 (ps)
> 
> this is the part of output mindist.xvg
> 
>         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
>         3        6.000  0.000  6.000  6.000  6.000
> 
> 
> 
> 
> 2. g_mindist -s full.tpr -f full.xtc -n index.ndx -pi -od mindist.xvg -max
> 
> Select a group: 19
> Selected 19: 'c-alpha-gly1'
> Reading frame   16610 time 8300.000
> 
> The shortest periodic distance is 6 (nm) at time 0 (ps)
> 
> 
> The part of output mindist.xvg
> 
>         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
>         3        6.000  0.000  6.000  6.000  6.000
> 
> 
> 
> The minimum distance is 6nm and it is exactly what is expected but there
> should also be distances more than 6nm (considering 26 periodic images). I
> don't know how to get that. Also i want to ask one more thing what is
> "maximum internal distance " which is probably indicated by the third
> column of mindist.xvg output.

Where are you reading about "maximum internal distance?"  I don't see that term 
(as quoted) anywhere in the g_mindist -h output.  Is this a separate concept? 
It probably refers to the maximum distance within the group, like an end-to-end 
distance, but that's just a guess.

Check the header information in your mindist.xvg file; typically explanations of 
all columns are presented there.  From g_mindist -h you will also see that the 
box vectors are printed to the output, so if you're in a 6-nm box, that's what 
you'll see in the last three columns, I'd be willing to bet :)

-Justin

> 
> Thanks
> 
> Regards
> 
> Alka
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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