On Thu, Sep 3, 2015 at 6:16 AM, Damiano Spadoni <enxds6.nottingham.ac.uk>
wrote:
> Dear AMBER creators,
>
> I'm trying to run the following script to simulate a heating step of my
> protein:
>
If you look at the bottom of the output file you attached, you'll see the
error message:
vlimit exceeded for step 330; vmax = 39.9816
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 1 728 26323 26322
Basically what this means is that your simulation blew up. You need to
investigate why that might have happened (it would help to print energies,
and if necessary coordinate frames, every step to get a more detailed view
of what is going wrong). Also, have a look at atoms 26323 and 26322 --
that is where your SHAKE failure is occurring.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 03 2015 - 05:30:03 PDT
