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
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