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