[gmx-users] truncated octahedron box vector angles and number of waters

[Tsjerk Wassenaar]

Hi Jlom,

The vectors depend on the orientation of the truncated octahedron, and on
which three out of all possible vectors are chosen. As for the difference
in water molecules, I don't know what AMBER does, but I can tell what
Gromacs does. You have the diameter of the system, 15.385 nm, to which
twice the 1.2 nm is added, giving the vector length 17.785 nm. A cube of
that length would have a volume of 5625 nm^3, and a truncated octahedron is
about 78% the volume of a cube, so it gives 0.78*(17.785**3) = 4388 nm^3.
Well, there's some rounding..., the 4330.63 will be correct. Solvating that
with genbox should give a pretty much correct amount of water. If AMBER
gives you so much less, I'd guess there's something odd there.

But, why not use a rhombic dodecahedron today?

Cheers,

Tsjerk


On Fri, Jun 13, 2014 at 2:02 PM, gromacs query <gromacsquery at gmail.com>
wrote:

> Dear All
>
> I am creating a truncated octahedron box and in vmd it appears as a
> rectangular box. In mailing list it has been suggested to use trjconv -ur
> compact option. But I have two issues,
>
> 1) I get box vector angle 70 90 70 with editconf and should be around 109
> 109 109 for a truncated octahedron box
>
> editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron
>
>     system size : 12.324 14.348  5.952 (nm)
>     diameter    : 15.385               (nm)
>     center      :  7.774  7.569  7.829 (nm)
>     box vectors : 12.324 14.348  5.952 (nm)
>     box angles  :  90.00  90.00  90.00 (degrees)
>     box volume  :1052.41               (nm^3)
>     shift       :  1.119  5.007 -0.568 (nm)
> new center      :  8.893 12.576  7.261 (nm)
> new box vectors : 17.785 17.785 17.785 (nm)
> new box angles  :  70.53 109.47  70.53 (degrees)
> new box volume  :4330.63               (nm^3)
>
> 2) I have a same system in AMBER and using truncated oct box with same 12
> Angstrom water buffer but in Gromacs I get almost twice water molecules as
> I get in AMBER but with AMBER I get 109 109 109 vector angles. Just to add
> in AMBER I used the default value of closeness of solvent molecules being
> 1.0 Angs. I am not sure whats default in editconf (though I see it uses
> default water density value)
>
>
> Please suggest why I am getting different vector angles and number of
> waters?
>
> best regards
> JIom
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-- 
Tsjerk A. Wassenaar, Ph.D.