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
That is correct.
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
That is correct, too.
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 anglesAm I misinterpreting the output? Does “size 3 clusters” refer to a cluster of 3 atoms
where only the 2 bonds are being fixed?
Yes.
Could you please tell me which combination is the right one to use for the TIP4P?
The first one. Fix shake has a special case for angles withe bonds fixed, too.
Axel