On Wed, 2015-09-16 at 11:06 +0200, Bala subramanian wrote:
> Jason,
> Thank you for the information,
>
> We reinstalled amber12 with all bug fixes carefully.I tried pmemd.cuda but
> it did not produce any error.
Then per my suggestion below, just run in serial.
> However a trial with serial sander and
> sander.MPI gave me the following error pasted below. I am trying to explore
> the forum for previous reports on the error.
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 371110.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 371110. NUM_NOSHAKE = 0 CORRECTED RNDFP = 371110.
> | TOTAL # of degrees of freedom (RNDF) = 371110.
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 3977265
> | TOTAL SIZE OF NONBOND LIST = 65149563
> vlimit exceeded for step 0; vmax = 594.4462
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 643 1307 1308
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
Your system blew up. There are lots of reasons this could happen. Note
that pmemd.cuda does not have vlimit checks, so it's likely that the
simulation blew up in pmemd.cuda as well, but it just never complained.
You will have to investigate why your system blew up like this.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 16 2015 - 05:30:06 PDT
