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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