Hi Francesco,
It's really hard to pinpoint the problem without more details. But what this
message is telling you, in general, is that your QM region is "expanding"
too far. QM atoms share one big pair list, and are not allowed to interact
with their periodic images. So, the QM region + cutoff must be kept smaller
than the box size.
(See a brief explanation in J. Phys. Chem. A 2007, 111, 5655-5664. A more
detailed explanation will be in an upcoming article)
This could be, as was suggested, one solvent molecule mistakenly included in
the QM region and that is diffusing away. It also did happen to me before
that, as the QM region moves, it assumes an extended position and suddenly
it's too large. Or, depending on the problem, you molecule could even
dissociate and then the parts separate too much.
Just to clarify one point, the QM region is recentered at every MD step, so
you don't have to worry about it diffusing out of the box, as long as it is
in one piece.
HTH,
Gustavo.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Francesco Pietra
> Sent: Saturday, August 04, 2007 4:33 AM
> To: Amber
> Subject: AMBER: Fwd: QM region + cutoff larger that box
>
> Although I suspected the problem does not arise from the box
> size, I have rerun md for the eq conformer. I started from
> prepin used successfully for the ax conformer in chcl3 and
> for both conformers in h2o. Setting the chloroform box 20A
> and md nstlim = 20,000.
>
> I have reexamined the min.in and md.in, they seem to be correct.
>
> It bombed at step 19150 with same indication "QM part +
> cutoff larger than box". As on previous runs, the mdcrd file
> shows the solute correctly immersed in molecules, allegedly
> chloroform. Say "allegedly" because of what said previously (below).
>
> Thanks
>
> francesco pietra
>
>
> --- Francesco Pietra <chiendarret.yahoo.com> wrote:
>
> > Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
> > From: Francesco Pietra <chiendarret.yahoo.com>
> > Subject: QM region + cutoff larger that box
> > To: Amber <amber.scripps.edu>
> >
> > QM-MM run successfully (20,000 steps) for axial
> methylcyclohexane in
> > chloroform along the lines of Tutorial A2 with Amber9.
> >
> > Equatorial methylcyclohexane also run successfully for
> 10,000 steps.
> > When I attemped to double nstlim (20,000), run bombed because QM
> > region + cutoff
> > (8.0)
> > larger than box (15.0). I repeated the run, instead of two
> consecutive
> > 10,000 steps, just a single run of 20,000 starting from where the
> > 10,000-step run had been successful. Same error bombing.
> out file for
> > the latter run attached. I can't grasp where my error is.
> >
> > An additional query: I was unable to delete chloroform from VMD.
> > Curiously, if I indicate to show carbon only, this is shown
> correctly
> > for the methylcyclohexane molecule, while chloroform is shown as an
> > ammonia-like umbrella with four identical atoms. I.e., chlorine is
> > shown as if it were carbon. Should I select a color for chlorine? I
> > was unable to trace where to deal with chlorine atom. I used the
> > chloroform box in Amber9.
> >
> > All that because I am checking convergence for ESCF with a simple
> > test, flexible molecule.
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> >
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Received on Sun Aug 05 2007 - 06:08:10 PDT
