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

[JW Feng]

David,

The results from using version 3.3.1 is different from version 3.3.2.

In version 3.3.1, adding "SOL OL 0" and executing "genbox -cs
tip5p.gro -box 1 1 1" created a box with 37 SOL molecules but the
density is too high at 3072.87 g/L.

In version 3.3.2, adding "SOL OL 0" did not work.  However, I added
"SOL  LP    0" to the end of vdwradii.dat and the resulting water box
contained 37 SOL molecules.  The density is incorrect at 2582.79 g/l.
This box contains six more SOL molecules compared to a box created
with TIP4P water.

JW

On 10/7/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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
> releases.
>
> --
> 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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-- 
Jianwen A Feng
Center for Computational Biology
Washington University in St. Louis