On Thu, Mar 01, 2018, ASMITA SEN wrote:
>
> vlimit exceeded for step 5804; vmax = 32.7330
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2333 4822 4823
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
As the message says, there is probably something wrong with the
simulation or force field. As a start, look at the region around atoms
4822 and 4823. Are these part of standard residues, or part of
something else, like the iron-containing moiety? See if you can look at
a restart file as close as possible to the time the SHAKE failure
happened, and look for problems (like very short non-bonded overlaps).
[The "checkoverlap" action in cpptraj can be very helpful here.]
Also, check the van der Waals radius of the hydrogen in the Fe-OH group:
if it is zero, that might lead to the sorts of problems you are seeing.
Of course, the problem might be somewhere else entirely.
...good luck...dac
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Received on Mon Mar 05 2018 - 05:30:03 PST
