I have come across an interesting problem with SHAKE in TI in Amber 11. I have been running tests using two protein-carbohydrate complex systems. My calculations crash immediately with the following error:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 1014 2057 2058
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
If ALL of the following are true:
1) The protein is present in the system (regardless of whether the mutation is occurring in the protein or in the bound ligand)
2) SHAKE is on
3) The total number of cpus the job is submitted to is >16
BUT
The same calculation runs without complaint if ONE of the following is true:
1) Only the carbohydrate ligand is present (i.e. Ti for the mutation in the free ligand)
2) SHAKE is turned off
3) The total number of cpus the job is submitted to is 16 or less
So basically, TI with a protein in the system will not run with SHAKE on if the job is submitted to >16 cpus. But it will run if I either turn SHAKE off or submit to16 or fewer cpus. A system containing only a carbohydrate in water runs with SHAKE on regardless of the number of cpus the job is submitted to, even if I solvate with a large enough box to give it a greater number of atoms than the protein-carboydrate complex system.
I have tested this on multiple machines with different architectures all running the release version of Amber 11 (fully patched), as well as the git version of AMBER from earlier today, and have gotten the same behavior. In case it could provide useful information, I tested for the non-power-of-2 number of cpus at which the run/crash threshold lies: 18 the protein system runs with SHAKE on; 20 it crashes.
Any thoughts?
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Received on Mon May 23 2011 - 19:00:02 PDT
