On Mon, Jun 18, 2012, DEBOSTUTI GHOSHDASTIDAR wrote:
>
> I had been running the system with dt=0.001. However, after 1ns
> simulation when I increased dt to 0.002fs, it crashed with the
> following error:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 5407 8261 8262
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
Does it immediately crash (i.e. on the first step where you have the increased
time step? Or sometime well into the simulation? It might help to look at
the system right before the SHAKE error occurs. It would also be of some help
to know if this is a standard system (protein/nucleic acid) or has
non-standard parts like ligands or cofactors; and if atoms 8261 and 8262 are
in (or close to) any non-standard region.
....dac
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Received on Mon Jun 18 2012 - 11:00:03 PDT
