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
>
>
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Received on Tue May 17 2016 - 12:30:03 PDT
