Hi Gustavo and Bud:
Yes, as you suspected, the run that failed had qmmask ='1-2' while there was
just one residue (initially I attached the out file, where the input file could
be seen). When qmmask is set correctly, even this run went to completion up to
tried 100ps.
The far more serious problem is how to run the QM part, i.e.
(1) which theory for the given problem,
(2) what to look at (ESCF, EPtot, ..) to compare the potential energies of the
conformers.
Semiempirical PM3 AM1 MNDO are known to be unable to reproduce conformational
energy differences between conformers. PM3, for example, gives for
methylcyclohexane eq/ax 1.0-1.1, against the experimental (non-hydroxylic
solvents r.t., 1.8). I am unfamiliar with PDDG or CARBI variants, though
probably they follow the trend of their precursors: where one performs better,
the other one fails. The trend being unpredictable.
On the other hand, DFT-MM as in Amber9 can't deal with the medium effect, which
is just my interest. Also, DFT requires very modern functionals and high basis
sets to work with my cases.
I am now exploring the performance of semiempirical QM-MM with test cases that
embody features of the molecules of my interest. The conformational ratios for
these test cases are known in condensed phase. I can't see how to approach the
case better for the time being.
Cheers
francesco pietra
--- Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> 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 Wed Aug 08 2007 - 06:07:14 PDT
