[gmx-users] Problem with -shell parameter of genbox

Nicolas Michel n.michel84 at wanadoo.fr
Thu Aug 15 10:57:06 CEST 2002

>Works like a charm on my laptop using MS-W2K and the binary Gromacs
>distribution from the website... Could you explain exactly what you
>did and perhaps copy over the exact error message(s) you got?

well, I certainly did something wrong!

Here are my commands and results:

editconf -f map.pdb -o map1.gro -d 0.5 -princ

->new system size  :  1.078 2.980 2.310
->      shift              :-9775.961-8964.926-932.629 (nm)
->new center         :  1.038 1.991 1.655 (nm)
->new box vectors :  2.078 3.980 3.310 (nm)
->new box angles  : 90.00 90.00 90.00 (degrees)
->new box volume  : 27.38                    (nm^3)

editconf -f map1.gro -o map1.pdb
->visualization with RasMol, the new molecule is oriented along the z axe.

genbox -cp map1.gro -cs -p map.top -o map1w.gro -shell 0.6
->program starts, generates tables and grid (8 x 16 x 13 cells), checks
overlaps and generates a new grid ( 6 x 13 x 11 cells) and then stops (10
seconds) and crashes...

Well, I've just tried on my old MS-W98 system and it works! I think there's
something wrong with MS-Wme.
I will check my Wme system and do my simulations under MS-W98.
Thank you and sorry to take your time...


Nicolas Michel
Doctorant en Chimie Organique
Laboratoire de Chimie BioOrganique et des Systemes Moleculaires Vectoriels

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