Hello,
I am currently carring out SMD siumaltions using the nscu_SMD function
of amber10. Prior to this, my systems have gone through minimiastion
and equilbration steps with no problems. I have even run seperate 20ns
of MD without any problems with sensible output---just to be sure its
not a 'minimisation' issue.
However, when carring out the SMD siumaltions on which i use 3pairs of
atoms for constant velocity pulling all seems to work fine until late
in the simulation when i get the error message below:
vlimit exceeded for step 80727; vmax = 33.2222
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 5 745 1522 1523
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
The odd thing is that sometimes the SMD simulations do go to
completion without the error and sometimes they dont...depending on
pulling velocity used!!!
Does this have anything to do with the 'restraints' imposed by
nscu_smd on the pair of atoms etc.....
at a loss as to the cause as i would have expected this type of error
during minimisation or very early in the MD.
cheers
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Received on Thu Jul 16 2009 - 10:08:44 PDT
