[gmx-users] genbox using tip5p water results in too few number of water molecules

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 7 20:21:39 CEST 2007

JW Feng wrote:
> Hello,
> I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC,
> TIP4P and TIP5P water with "
> genbox -cs <water model>.gro -box 1 1 1".  The TIP5P box contains half
> the number of water molecules compared to TIP4P and SPC.
> SPC:   33 SOL molecules, density=987.205 (g/l)
> TIP4P:  31 SOL molecules
> TIP5P:  15 SOL molecules
> Can anyone please explain this?  How do I get genbox to create a box
> with the right number of TIP5P water molecules.
> Thanks,
> JW
It is because of the name of the lone pairs (OL) which is interpreted as 
an oxygen atom. You can add OL in vdwradii.dat with radius 0 and try 
again. Please report whether it works, then I will fix it in further 

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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