AMBER Archive (2007)

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

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Mon Aug 06 2007 - 10:38:19 CDT

Hi Francesco,

The manual is right: The DFTB/SCC-DFTB implementation in Amber9 does *not*
support GB, PME or Ewald. Support for Ewald and PME are already in Amber10,
and we are working on GB. Hopefully, by the release date, all that will be
included in Amber10.

However, that does *not* mean that the DFTB implementation in Amber9 cannot
deal with medium effects. The effect of the environment is taken into
account, since the SCF is done in the presence of the MM atoms as point
charges. However, it (Amber9) does not support the Ewald/PME methods for the
long range interactions, so you would need to use a larger cutoff. (BTW, I'm
assuming that by "DFT-MM in Amber9" you meant the SCC-DFTB method.)

Gustavo.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Francesco Pietra
> Sent: Monday, August 06, 2007 11:07 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Fwd: QM region + cutoff larger that box
>
> 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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>
>
>
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