[gmx-users] TIP5P - dummies sit on top of each other
Justin A. Lemkul
jalemkul at vt.edu
Tue May 12 14:30:03 CEST 2009
ilona.baldus at bioquant.uni-heidelberg.de wrote:
>
> Hi,
>
> I am trying to change my ice crystal from a three-site water model to
> the TIP5P water model. For that I use pdb2gmx. The program adds the two
> dummy atoms, but they are at exactly the same position as the oxygen and
> not two additional sites as stated by the paper and also as I find in
> the file /gromacs/top/tip5p.gro.
>
> For a small ice crystal my problem looks like this:
>
> Original ice.gro file:
>
> Groningen Machine for Chemical Simulation
> 24
> 2 SOL OW 1 0.000 0.000 0.000
> 2 SOL HW1 2 0.000 0.000 0.096
> 2 SOL HW2 3 0.078 0.045 -0.032
> 3 SOL OW 4 0.224 0.129 -0.091
> 3 SOL HW1 5 0.224 0.129 -0.187
> 3 SOL HW2 6 0.302 0.084 -0.059
> 4 SOL OW 7 0.224 0.387 0.000
> 4 SOL HW1 8 0.146 0.433 -0.032
> 4 SOL HW2 9 0.224 0.297 -0.032
> 5 SOL OW 10 0.000 0.517 -0.091
> 5 SOL HW1 11 -0.078 0.472 -0.059
> 5 SOL HW2 12 0.000 0.607 -0.059
> 6 SOL OW 13 0.000 0.000 0.274
> 6 SOL HW1 14 -0.078 0.045 0.306
> 6 SOL HW2 15 0.000 -0.090 0.306
> 7 SOL OW 16 0.224 0.129 0.365
> 7 SOL HW1 17 0.146 0.084 0.333
> 7 SOL HW2 18 0.224 0.219 0.333
> 8 SOL OW 19 0.224 0.387 0.274
> 8 SOL HW1 20 0.224 0.387 0.178
> 8 SOL HW2 21 0.302 0.433 0.306
> 9 SOL OW 22 0.000 0.517 0.365
> 9 SOL HW1 23 0.000 0.517 0.461
> 9 SOL HW2 24 0.078 0.472 0.333
> 0.44744 0.77499 0.73067
>
>
> Modified (supposedly tip5p) .gro file:
>
> Groningen Machine for Chemical Simulation
> 40
> 1HO5 HW1 1 0.000 0.000 0.096
> 1HO5 HW2 2 0.078 0.045 -0.032
> 1HO5 OW 3 0.000 0.000 0.000
> 1HO5 HW3 4 0.000 0.000 0.000
> 1HO5 HW4 5 0.000 0.000 0.000
> 2HO5 HW1 6 0.224 0.129 -0.187
> 2HO5 HW2 7 0.302 0.084 -0.059
> 2HO5 OW 8 0.224 0.129 -0.091
> 2HO5 HW3 9 0.224 0.129 -0.091
> 2HO5 HW4 10 0.224 0.129 -0.091
> 3HO5 HW1 11 0.146 0.433 -0.032
> 3HO5 HW2 12 0.224 0.297 -0.032
> 3HO5 OW 13 0.224 0.387 0.000
> 3HO5 HW3 14 0.224 0.387 0.000
> 3HO5 HW4 15 0.224 0.387 0.000
> 4HO5 HW1 16 -0.078 0.472 -0.059
> 4HO5 HW2 17 0.000 0.607 -0.059
> 4HO5 OW 18 0.000 0.517 -0.091
> 4HO5 HW3 19 0.000 0.517 -0.091
> 4HO5 HW4 20 0.000 0.517 -0.091
> 5HO5 HW1 21 -0.078 0.045 0.306
> 5HO5 HW2 22 0.000 -0.090 0.306
> 5HO5 OW 23 0.000 0.000 0.274
> 5HO5 HW3 24 0.000 0.000 0.274
> 5HO5 HW4 25 0.000 0.000 0.274
> 6HO5 HW1 26 0.146 0.084 0.333
> 6HO5 HW2 27 0.224 0.219 0.333
> 6HO5 OW 28 0.224 0.129 0.365
> 6HO5 HW3 29 0.224 0.129 0.365
> 6HO5 HW4 30 0.224 0.129 0.365
> 7HO5 HW1 31 0.224 0.387 0.178
> 7HO5 HW2 32 0.302 0.433 0.306
> 7HO5 OW 33 0.224 0.387 0.274
> 7HO5 HW3 34 0.224 0.387 0.274
> 7HO5 HW4 35 0.224 0.387 0.274
> 8HO5 HW1 36 0.000 0.517 0.461
> 8HO5 HW2 37 0.078 0.472 0.333
> 8HO5 OW 38 0.000 0.517 0.365
> 8HO5 HW3 39 0.000 0.517 0.365
> 8HO5 HW4 40 0.000 0.517 0.365
> 0.44744 0.77499 0.73067
>
> Is that a known error? What can I do
>
This is the expected behavior, given the description in the manual (section
5.6.2, page 103):
10 three water “hydrogens”
two hydrogens are generated around atom i according to SPC [57] water geometry.
The symmetry axis will alternate between three coordinate axes in both
directions. In addition an extra particle is generated on the position of the
oxygen. This is for use with four-atom water models such as TIP4P [79]
10 four water “hydrogens”
Same as above, except that two additional particles are generated on the
position of the oxygen. This is for use with five-atom water models such as TIP5P
[85]
The second entry should be addition type 11, not 10, I believe.
-Justin
> Best wishes,
>
> Ilona
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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