[gmx-users] genbox and interatomic distances

[Anton Feenstra]

Markus O Kaukonen wrote:
> 
> Dear *,
> 
> I try to generate a 3x3x3 nm simulation box filled with 788
> non-overlapping water molecules by saying
> 
> genbox -try 1000 -ci spc1.pdb -vdwd 0.10 -box 3 3 3 \
> -nmol 788 -o 788H2O.pdb
> 
> I have removed the file vdwradii.dat
> 
> However, in the output file water molecules are often closer than 0.2 nm.
> 
> How I done something wrong
> or is genbox the tool to do this job,
> or does it only check solute-solvent distances ?

I thought it uses a certain fraction of the sum of vdw radii, e.g.
0.8*(0.1+0.1) for the minimum distance. But after checking the 
source, it seems to do what it says: the sum of vdw radii is used.
(The relevant routines are in src/tools/addconf.c). You say you
removed vwdradii.dat, can you also see that the line that says
that a library file is being opened, no longer is printed?
Gromacs can be very inventive in searching for it's library
files... ;-)

> Any other tool to do the job?

No other tool that I know of, but why not replicate the spc216 box
to get your 3x3x3 nm box? genbox will also fo that for you...
If you're not happy with the way spc216.gro looks, you could cook
it at 1000K for a few ps... ;-)

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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