also look in the section where sander first reads and reports the
restraints and see what it thinks the current and target values are.
On Tue, Feb 7, 2012 at 11:46 AM, Jason Swails <jason.swails.gmail.com>wrote:
> There are lots of reasons this can happen. If you set your NMR restraints
> too far away from their current value, it will impose a huge force that
> will put a severe strain on your system (you'll get integration failures,
> which can result in SHAKE failures).
>
> Try printing out the trajectory more frequently (if you can reproduce this
> error) and see what happens between atoms 2508 and 2509.
>
> HTH,
> Jason
>
> On Tue, Feb 7, 2012 at 10:19 AM, Rahul Banerjee <
> rahul.banerjee.chemistry.msu.edu> wrote:
>
> > Dear All,
> >
> > I was running Amber MD (with Sander) simulation for a NMR structure with
> > all the NMR restraints. During heating cycle I encountered following
> error
> > at the end of my output file:
> > ##############################################################
> > vlimit exceeded for step 331127; vmax = 20.0590
> > vlimit exceeded for step 331130; vmax = 21.4621
> > vlimit exceeded for step 331140; vmax = 43.9731
> > vlimit exceeded for step 331141; vmax = 248.8721
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 1 1265 2508 2509
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> > ##############################################################
> >
> > Looking at the structure I don't see any obvious reason why the program
> > crashed in this way.
> >
> > Can anybody suggest any clue for this?
> >
> > Thank you in anticipation.
> >
> > With best regards,
> > Rahul
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 07 2012 - 09:30:02 PST
