[gmx-users] size of the system

Mark Abraham mark.abraham at anu.edu.au
Wed Mar 12 00:02:36 CET 2008

> It seems my answer to Berk was processes by the system
> in a wrong way.
>>  guess this procedure should work, so this might be a bug.
>> But you are making things much more complicated than needed.
>> You can skip the first two steps and just use the -box option of genbox
>> instead of -cp.
>> Berk.
> OK.
> genbox -cs spc216.pdb -box 3 3 3.

The correct file to use is spc216.gro (which genbox automatically finds in
the GROMACS $GMXLIB/top directory). I'm guessing that genbox is finding a
local spc216.pdb which is somehow broken.


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