On Mon, Jan 05, 2015, Anupam Goel wrote:
>
> I am running a nocut MD using
> polyAT_gb_md1_nocut.in<http://polyat_gb_md1_nocut.in> as shown here
> http://ambermd.org/tutorials/basic/tutorial1/section4.htm and get the
> following error.
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 60 97 98
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> Can you suggest which deviation is being talked about in the error?
The easiest thing here is to check your polyAT_gb_md1_nocut.out file against
the one that is provided in the tutorial. Look for differences -- I'm
guessing that these will arise even in the first energies that are printed
out. Also, try the 12 Ang. cutoff run, to see if that works.
If you do get energy differences at the first step of MD, do the same thing
for the minimization: check your minimization outputs vs. those provided
in the tutorial.
(For your initial question: the bond between atoms 97 and 98 is giving the
problem, but that information is unlikely to be of much help in figuring out
what went wrong.)
...good luck...dac
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Received on Mon Jan 05 2015 - 15:00:02 PST
