[gmx-users] TIP5P - dummies sit on top of each other
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 12 15:34:36 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.
>
Check again after 1 step of MD.
> 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
>
> Best wishes,
>
> Ilona
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
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
More information about the gromacs.org_gmx-users
mailing list