Hello all,
I am trying to set up a simulation of water using the TIP4P model. Therefore, I need to use the
SHAKE command to fix both BONDS and ANGLE. I followed the documentation, but I am having
some doubts about interpreting if I am doing things correctly. This is why.
I have 3184 water molecules.
The OH bond in my water molecule is labeled type 3, i.e. “b=3”.
The angle in my water molecule is labeled type 4, i.e. “a=4”.
- Following the command page, in order to fix both the two OH bonds and the angle I should use:
fix shakefix WATER shake 0.00001 500 0 b 3 a 4
but this gives me the following output:
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
3184 = # of frozen angles
Based on the output, I would say that only the angles are being constrained.
So, I tried the following different command:
- fix shakefix WATER shake 0.00001 500 0 b 3
and this gives me the following output:
0 = # of size 2 clusters
3184 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
Am I misinterpreting the output? Does “size 3 clusters” refer to a cluster of 3 atoms
where only the 2 bonds are being fixed?
Could you please tell me which combination is the right one to use for the TIP4P?
Thank you very much in advance for your time and help.
Best regards,
Francesco Rizzi