On Wed, May 16, 2012, Urszula Uciechowska wrote:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 8 14 192 190
>
You can look at your structure around atoms 192 and 190: is there anything odd
there? Is the energy on the first step of MD the same as on the last step of
minimization? SHAKE problems are generally the result of some underlying
problem with the system. You might use the "checkoverlap" command in ptraj to
see if either of these atoms (or any pair of atoms) have short contacts.
It's possible that reducing the value of dt to 0.001 (or even 0.005) might
help, although that is rare. Certainly, you should try this with short runs
(say nstlim=10) with ntpr=1 to get the most information.
...good luck...dac
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Received on Wed May 16 2012 - 15:30:04 PDT
