[gmx-users] question about genbox -vdwd

Qiao Baofu qiaobf at gmail.com
Mon Feb 12 13:33:38 CET 2007

Hi all,

I have one question: when I use the "genbox -nmol 300 -ci a.gro -cp b.gro"
to insert a.gro into b.gro, for some system it gives good results,
while not for others.
On the other hand, the -vdwd opinion seems not work. I looked at the
code of gmx_genbox.c, but didn't find the reason.

>From the google, I found the following. The problem is the same as
mine. Who has good suggestions?

Thanks in advance!

>*The resulting output contains atoms which are too close. The distance
*>*between the atoms is sometimes
*>*as small as 0.01 nm which is smaller than the vanderwaals radii from the
*>*database vdwradii.dat . Not
*>*surprisingly, therefore I get errors when I run energy minimization or mdrun.
*>*  The output keeps repeating the message "tested 0 pairs,  removed 0 atoms
*>* " as I quote below.  I would
*>*greatly appreciate if somebody could guide me how to use genbox properly.
genbox isn't that good at randomly placing molecules within a box in cases
like this (are some emails in the archive on this).  It needs a bit of
work.  I use an in house program to do it, works out much better.  Although
I don't have it to give out to anyone, since it is part of a much larger
package that does a lot of other things and isn't mine to make available.
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