[gmx-users] choosing box vectors

[Justin Lemkul]

On 6/14/13 7:37 PM, gromacs query wrote:
> Dear Justin,
>
> Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
> dont want to use as I think they are wrong). In my case if I have already
> water molecules in my system then if I use:
>
> editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic
>
> even now also I see pbc box (in vmd) its quite big than system as you can
> see from output
>
>      system size : 10.707 11.077  7.493 (nm)
>      diameter    : 14.737               (nm)
>      center      :  6.928  6.932  6.936 (nm)
>      box vectors :  0.000  0.000  0.000 (nm)
>      box angles  :   0.00   0.00   0.00 (degrees)
>      box volume  :   0.00               (nm^3)
>      shift       :  0.441  0.436  0.432 (nm)
> new center      :  7.369  7.369  7.369 (nm)
> new box vectors : 14.737 14.737 14.737 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  :3200.60               (nm^3)
>
>
> What should I do?
>

You're specifying a cubic box, but for most membrane systems, that's probably 
wrong.  What editconf is doing is determining what box vectors are necessary, 
then since you're telling it to make the box cubic, it's forcing all of the 
vectors to be the same.  Apparently you have at least one dimension that, in 
this case, is 14.737 nm in length, and then all other vectors are then set to 
the same value.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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