[gmx-users] genbox overlap checking

[Roman Holomb]

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

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