[gmx-users] genbox using tip5p water results in too few number of water molecules
jw.a.feng at gmail.com
Sun Oct 7 21:55:28 CEST 2007
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.
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
> 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
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