[gmx-users] genbox and interatomic distances

[Markus O Kaukonen]

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 ?
Any other tool to do the job?

Best Wishes, Markus


-- 
++++++ OFFICE ++++++++++++++++++++++++++++++++ HOME ++++++++++++
Markus.Kaukonen at helsinki.fi   \          Verajakallionkatu 6 a 5
Helsinki Bioenergetics Group   \_______  02600 Espoo, Finland
Institute of Biotechnology             \ tel:+358-(0)9-5127122/h
Biocenter 3, P.O.BOX 65 (Viikinkaari 1) \____
FIN-00014 University of Helsinki              \______ H+ ______
tel: +358-(0)9-19159752/o, fax: +358-(0)9-19158001               \
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---