[gmx-users] genbox overlap checking

[Daniela S. Mueller]

hi roman, 

On Thu, 2006-03-09 at 17:14 +0100, Roman Holomb wrote:
> Dear all,
> 
> I have problem with using genbox
> When I try to add more than 20 BF4 molecules in the box (3.2 3.2 3.2) by
> 
> genbox -ci BF4_1.gro -nmol 20 -box 3.2 -o BF4_20.gro

probably you need to indicate a bigger van der waals distance by -vdwd
for your insert. 

as an alternative, why don't you stack your molecule with genconf? then
each molecule has as much space as in the unit box. 

regards,
daniela


> I usualy have connected BF4 molecules. Changes in the vdwradii.dat file
> not help.
> 
> Also during adding molecules I can see something like:
> 
> -----------------------------
> "Going to determine what solvent types we have.
> There are 0 molecules, 5 charge groups and 5 atoms
> There are 0 optimized solvent molecules on node 0
> There are 0 optimized water molecules on node 0
> Grid: 4 x 4 x 4 cells
> nri = 7, nrj = 10
> Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
> Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
> Try 1box_margin = 1.56!
> Removed 0 atoms that were outside the box
> nri = 7, nrj = 10
> Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
> Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.
> Try 2box_margin = 1.56)!
> ---------------------
> 
> 
> So ... overlap testing seem not work .... but why???
> 
> Any suggestion?
> 
> Sincerely
> Roman
> 

-- 

Daniela S. Mueller

biologist (Diplom, German degree)
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