it might help if you post the mdin and script that generated this output.
also include the head and tail of the restart file, if that was the inpcrd.
On Tue, May 17, 2016 at 3:27 PM, Thomas Pochapsky <pochapsk.brandeis.edu>
wrote:
> The .prmtop, .crd and .rst files are all "legacy" from (successful? at
> least completed) AMBER 11 runs. I am currently trying to run with a set
> of RDC restraints, with freezemol=true, to optimize the alignment
> tensor. Where do I find the box dimensions?
> thanks,
> tom p.
>
> On 5/17/16 3:01 PM, Carlos Simmerling wrote:
> > how did you generate this input structure? I might be wrong but it looks
> to
> > me that it thinks you have a negative box dimension.
> >
> > On Tue, May 17, 2016 at 2:45 PM, Thomas Pochapsky <pochapsk.brandeis.edu
> >
> > wrote:
> >
> >> Dear all,
> >>
> >> I am taking some .prmtop and .rst files that worked using AMBER 11, but
> >> am having trouble with maxing out the NONBOND LIST size in Amber 14.
> >> Here is what I am seeing if I cut the nonbonded interactions to 8 Å:
> >>
> >> | # of SOLUTE degrees of freedom (RNDFP): 149324.
> >> | # of SOLVENT degrees of freedom (RNDFS): 0.
> >> | NDFMIN = 149324. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 149324.
> >> | TOTAL # of degrees of freedom (RNDF) = 149324.
> >> ---------------------------------------------------
> >> 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 = 0.8332E-11 at 2.782960
> >> ---------------------------------------------------
> >> | Local SIZE OF NONBOND LIST = 15160735
> >> | TOTAL SIZE OF NONBOND LIST = 15160735
> >> Cutoff list exceeds largest sphere in unit cell!!
> >> Big problems with imaging!!
> >> a,b,c = -1244.71951386096 -1184.70414062345
> >> -1127.43981723746
> >> alpha,beta,gamma = 90.0000000000000 90.0000000000000
> >> 90.0000000000000
> >> cutlist,sphere = 10.0000000000000 -1778.43173586094
> >>
> >>
> >> If I leave the cutoff at 16Å, the program crashes because the non-bonded
> >> list is too large. Is there some file that I don't have write access to
> >> that stores NBs? This is a solvated simulation. If this is a simple
> >> problem, great, if not, I can provide more info upon request.
> >>
> >> Thanks,
> >> Tom Pochapsky
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
> _______________________________________________
> 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 May 17 2016 - 13:00:03 PDT
