> I am running a simple MD equilibration with CN- and K+ ions in ~500 H2O.
> When I have 1 CN-K+ in the system, it works perfectly. But, the moment I
> have 2K+CN- in H2O the SHAKE (ntc=3, ntf=3) is giving me this error:
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 2966 5 6
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I have tried increasing the temperature and decreasing it in order to
> remove strains in the system (as suggested in the amber mailing list to
> someone in past). Also, I have tried changing the system size and
> equilibriation at constant pressure and also at constant volume. Everything
> works fine for 1CN-K+/H2O but nothing works for 2K+CN-/H2O.
If you get to the error point, then rerun the last simulation with
ntwx=1 or nstlim = step before failure, you will be able to see
what the problem is with this configuration by watching mdcrd as a
movie or making a pdb from the restrt.
Bill
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Received on Fri Sep 02 2011 - 21:30:02 PDT
