Yes, you should send the actual input files you used. You should also try
and narrow down what part of the system is blowing up. This type of effect
is usually due to vdw clashes, or something of the like (non-bonded
interactions). Did you visualize your system? Could you find anything
wrong with it (that is usually the first place you should start)?
If you can't find what part of the system is blowing up, you can run a
sander minimization for 1 step (maxcyc=1), and the information about the
gradient (I expect it will be very large) will give you an indication of
where to look.
Others may chime in with their advice.
Good luck!
Jason
On Thu, Jun 17, 2010 at 9:02 PM, Homa Azizian <homa.azizian.anu.edu.au>wrote:
> Bill,
> I heat the system step by step from 0 to 308 K for about 20 ps, after
> minimizition.
> the below message came after 48 ns. also my system is a dimer protein with
> one ligand.
>
> vlimit exceeded for step 0; vmax = 388.4665
> vlimit exceeded for step 1; vmax = 399.4700
> vlimit exceeded for step 2; vmax = 387.9217
> vlimit exceeded for step 3; vmax = 352.8459
> vlimit exceeded for step 4; vmax = 32817.3873
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 302 606 607
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> should I send another information?
> Regards,
> Homa
>
> ----- Original Message -----
> From: Bill Ross <ross.cgl.ucsf.EDU>
> Date: Thursday, June 17, 2010 3:39 pm
> Subject: Re: [AMBER] problem with the energetics of the system
> To: amber.ambermd.org
>
> > > Here is my input file.
> > > imin = 0, irest = 1, iwrap=1 ,ntx = 5,
> >
> > How did you equilibrate?
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jun 17 2010 - 18:30:05 PDT
