AMBER Archive (2007)

Subject: Re: AMBER: Fwd: QM region + cutoff larger that box

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Aug 06 2007 - 10:07:09 CDT

Hi Bud:

Thanks. I was mislead by the statement on Amber9 manual "does not currently
support generalized Born, PME or Ewald". I have just emailed the signed form
requesting the required files for scf-dftb. We will see.

Not yet traced the ref to your publications using scc-dftb, though it will be
easy.

Cheers

francesco pietra

--- "M. L. Dodson" <mldodson_at_houston.rr.com> wrote:

> Francesco Pietra wrote:
>
> > 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
> >
> >
>
> I have been using DFTB/SCC-DFTB with or without the dispersion
> corrections (read the papers). This has the reputation of being
> very good for QM treatment of chemical reactions in enzyme active
> sites. This is not very different in concept from your interests
> in solvent effects. Are you sure this is an inadequate method?
> This approach is fairly different from DFT calculations in, e.g.,
> Gaussian. I'm sure others can offer their impressions as well.
>
> In my understanding, the dispersion corrections to DFTB/SCC-DFTB
> are used to apply corrections for Van der Waals interacting
> systems such as nucleic acids base pair stacking computations.
>
> The energy of the system needs to be calculated by averaging over
> an ensemble of structures as is always true for MD. The ensemble
> is sampled by the dynamics, so the runs have to be "long enough"
> to adequately sample the ensembles. How long is "long enough"
> could serve as the definition of a "hard problem".
>
> Good luck,
> Bud Dodson
>
> >
> >
> >
> > --- Gustavo Seabra <gustavo.seabra_at_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_at_scripps.edu
> >>> [mailto:owner-amber_at_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_at_yahoo.com> wrote:
> >>>
> >>>> Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
> >>>> From: Francesco Pietra <chiendarret_at_yahoo.com>
> >>>> Subject: QM region + cutoff larger that box
> >>>> To: Amber <amber_at_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
> >>>>
>
> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-five_63-386_one
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