[gmx-users] genbox using tip5p water results in too few number of water molecules
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 8 20:31:43 CEST 2007
JW Feng wrote:
> 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.
that is a coincidence. try with a larger box. the number is correct.
> On 10/7/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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