GROMACS 5 - problem with LINCS with freeze groups
I have experienced some strange behaviour.
I am running test simulation to check freeze groups in gromacs-5.0.2 (using amber03w ff with TIP4P2005 water).
And I am getting LINCS Warnings for atoms which should be frozen...
Same situation is with Gromacs-4.6.7, but in Gromacs-4.6.5 simulation runs O.K.
I have attached grompp files.
#1 Updated by Berk Hess over 3 years ago
- Status changed from New to Accepted
- Assignee set to Berk Hess
The issue is with the combination of three things: freeze-groups, constraints and twin-range interactions.
Solution 1: If you want to freeze the whole protein, you should not also constrain it, use constraints = none.
Solution 2: You are using twin-range interactions, which I don't know if that's on purpose. This can easily happen accidentally. You can set rcoulomb and rlist equal to rvdw=1.2. This will make the simulation slower, but more accurate.
I don't know if it is worth fixing this bug, since twin-range interaction are only supported with the group scheme, which is already deprecated.