[gmx-users] genbox problem

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 8 19:15:48 CET 2006

Roman Holomb wrote:
> Dear Gromacs users,
> I use genbox for random insert 100 BF4 molecules in the box. But there are
> so many connections between BF4 anions ..... I have decreased number of
> molecules to 20 but I have the same problem. Sometimes this can be fixed
> by energy minimization. After optimization I have no connections between
> different BF4 anions but there are small amount of BF4 with F-F bonds.
> This is realy problem to use "genbox" for generate the model (I plan to
> make more complicated systems and I have no posibility to correct models
> "by hand"
> So my question is: Can I do something with parameters (VDW coulomb
> distance) to get correct results from genbox? Seems nothing influence here
> .....

edit vdwradii.dat

> Thanks
> Sincerely
> /Roman
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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