I have a similar chronic problem in Amber10. I routinely run with qmcut = cut = 9.0 because of this. I plan to work with Ross to fix this as soon as 11 is released.
Bud Dodson
On Apr 20, 2010, at 11:36 AM, aapeters.ncsu.edu wrote:
> Hello users
>
> When using Amber10 QM/MM I get errors complaining my box is too small.
>
> But when I look at the structure and at the QM region coordinates, there
> seems to be enough space. There seems to be a conflict between the
> coordinate extremes written out in the first part of the output file (or
> the qmmm_region.pdb file), and the bounds written out in the latter part
> of the output file:
>
> ERROR: QM region + cutoff larger than box dimension:
> QM-MM Cutoff = 4.0000
> Coord Lower Upper Size Radius of largest sphere inside unit
> cell
> X -5.632 13.150 18.782 11.146
> Y -5.431 13.671 19.102 11.146
> Z -15.168 14.794 29.962 11.146
>
> To hone in on the problem, I set up a run that crashes on the second step.
> So
> 1) the initial qm region positions are written in the output file
> 2) the system takes one step, and writes "qmmm_region.pdb", the
> corresponding pdb file
> 3) the system crashes on the 2nd step, writing the bounds violation in the
> output file.
>
> Assuming positions barely change in one step, there seems to be a
> significant conflict within the code about where it thinks the bounds are?
>
> I attached the output files
>
> Thanks in advance for any help.
>
> Andrew Petersen<junk.out><qmmm_region.pdb><J070.TI1.1.prm><K16qmmm.1.in>
>
--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Tue Apr 20 2010 - 10:30:03 PDT
