JW Feng wrote:
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.
that is a coincidence. try with a larger box. the number is correct.
JW
On 10/7/07, David van der Spoel <[EMAIL PROTECTED]> 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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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David.
________________________________________________________________________
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
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