[gmx-users] TIP5P - dummies sit on top of each other

[ilona.baldus at bioquant.uni-heidelberg.de]

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

Best wishes,

Ilona