[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:
> 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.
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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