[gmx-users] octahedron box shape problem
stockn at kfunigraz.ac.at
Wed Oct 31 17:40:59 CET 2001
On Wed, 31 Oct 2001, Erik Lindahl wrote:
> thomas stockner wrote:
> > Hi
> > I am trying to generate an octahedron or dodecahedron box for a MD
> > simulation, but unfortunately I am not succesful. I get only rectangular
> > boxes.
> > I am using Gromacs version 3.0.5
> > applying a commands like:
> > -editconf -f struc.g96 -o box.g96 -d 1.4 -bt octahedron -label A
> > -genbox -cp box.g96 -cs spc216.gro -o h2o.g96 -p struc.top
> > and creating a pdb file for visualizing with rasmol
> > -pdb2gmx -f h2o.g96 -o rasmol.pdb
> > the box I get is always recangular, independenty which options of editconf I
> > tryed (-bt; -angles; -box).
> > I don't understand, why the output of editconf regarding the box statistic
> > does not correspond to characteristics of the filled water box of the pdb
> > file visualised with rasmol.
> > I cannot find the error I make. Could anyone help me to generate an
> > octahedron box.
> Hi Thomas,
> What does the last line of the .gro file look like? If there are nine numbers
> and more than three of them are non-zero the box is probably correct.
thanks for the hint. I already checked the possibility, that my viewer
could show me the box in a wrong way. Unfortunately is was not the case,
as I check with ngmx and i filled the box with water molecules for
visualizing its borders.
the last lines of the structure file are:
$ tail h2o.g96
7098 SOL OW 21890 6.587239742 5.620179653 4.878179550
7098 SOL HW1 21891 6.524239540 5.548179626 4.847179890
7098 SOL HW2 21892 6.680239677 5.584179878 4.878179550
7099 SOL OW 21893 0.252369881 6.039179802 4.415120125
7099 SOL HW1 21894 0.193369865 6.119179726 4.419119835
7099 SOL HW2 21895 0.267369270 6.004179955 4.508120060
6.633870125 6.254472733 5.416532040
the output of editconf is:
diameter : 3.834 (nm)
center : 2.220 3.577 0.823 (nm)
box vectors : 0.100 0.100 0.100 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 0.00 (nm^3)
shift : 1.097 -0.450 1.885 (nm)
new center : 3.317 3.127 2.708 (nm)
new box vectors : 6.634 6.634 6.634 (nm)
new box angles : 70.53 109.47 70.53 (degrees)
new box volume : 224.74 (nm^3)
> I don't know right off, but one possibility is that the gromacs box
> really is an octahedron but it doesn't show in your viewer program.
> ngmx can show the different box types if you select it from one of
> the menus. Note however that the water molecules might not all
> be drawn within the box before you have performed any simulation,
> and that might cause it to look like the box isn't right.
additionally i made a short md run in order to get a trajectory for using
ngmx. again the box is rectangular. when trying change the box shape to
octahedron in get the error message:
"Can not change rectangular box to truncated octahedron"
it seem like as a truncated octahedron box was never created. or could it
be that genbox changes again the border definitions??
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