Thank you for the information.
I visualized the trajectory but nothing seemed strange reg. the reported
atoms 1307 and 1308, these atoms were Nz of LYS and one of the hydrogen
connected to it. Actually this problem occurred not at the beginning, but
after 100ns production run. I tried running a short 50ps simulation with
0.5fs time step to relax any severe clash and then continued the production
and then switched to 2fs. Now it is running fine.
On Wed, Sep 16, 2015 at 2:56 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Sep 16, 2015, Bala subramanian wrote:
> >
> > However a trial with serial sander and
> > sander.MPI gave me the following error pasted below.
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 0 643 1307 1308
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
>
> As the error message indicates, the problem is somewhere else. If the test
> cases work, then you probably have bad energies, but we have no
> information to
> help very much in tracking this down. Did you run energy minimzation
> before
> trying MD?
>
> ...dac
>
>
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--
C. Balasubramanian
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Received on Thu Sep 17 2015 - 03:00:03 PDT
