On Mon, Jun 17, 2013 at 6:20 PM, Hailin Huang <hailin.huang.my.liu.edu>wrote:
> Dear Amber Users,
>
> When I was running the density equilibration of a protein, calculations
> terminated at Nstep=12500 and I got this message "Nonbond cells need to be
> recalculated, restart simulation from previous checkpoint. with a higher
> value for skinnb". What is skinnb? Has anyone come across this problem
> before? The input follows:
>
This 'error' results from the simulation cell shrinking a lot (your
starting box was way too big). The system is divided into cells for
performance reasons, and if the cells shrink too much, then they become
smaller than the region defined by the cutoff. This breaks energy
conservation and creates a whole host of other problems.
I would suggest leaving skinnb alone (you can see what it does in the Amber
manual), and just restart the simulation from the last good restart file as
suggested. This will recalculate the nonbonded cells, getting rid of the
problem.
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=1000000,dt=0.002,
> ntc=2,ntf=2,
> ntb=2, ntp=1, taup=1.0,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> ntr=1, restraintmask=':1-106',
> restraint_wt=2.0,
> /
>
> The minimization of this structure showed the "RESTARTED DUE TO LINMIN
> FAILURE" message but it finished normally. This seems like a common error
> occurred in minimization and it wouldn't affect running MDs, but did it
> cause the above "skinnb" problem?
>
These are unrelated issues. The LINMIN failures are only important if you
need a true local minimum.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 17 2013 - 17:00:02 PDT
