Hi all,
Having used AM1/d-PhoT rather extensively, I have found it to be somewhat
numerically sensitive to physically large (as in spread out) QM regions. I
don't know if this is unique to the d-orbital implementation (which is
different from the normal sp-orbital NDDO code) or a general characteristic
of NDDO. I would give PM6 or MNDO/d a try, as those should also use
d-orbitals for phosphorous (although I would have to double check that in
the code to be sure).
Regards,
Brian
P.S. The are virtually no assurances that AM1/d-PhoT is a good model for
nucleobases, as these are entirely outside of the training set. Although
the nitrogen parameters are untouched from AM1, the changing of the C, O,
and H parameters certainly could have unbalanced some very important
effects when it is present. That being said, I'm pretty sure that
AM1/d-PhoT predicts superior proton affinities (wrt experiment) for small
organic compounds compared to AM1, which might salvage some of the effects
you are looking for.
On Wed, Nov 14, 2012 at 1:41 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> Hi,
>
> On Nov 14, 2012, at 2:15 PM, Vojtech wrote:
>
> > I have also tested another two SE methods (SCC-DFTB and AM1) and did not
> > observe that problem.
>
> Ok, this *may* be an indication that the SE method you've chose does not
> work very well for your system.
>
> > Furthermore, could you please explain me little bit more what do you
> mean by
> > 'parametrization of QM region'?
>
> Although its not very clear, sander *does* need parameters for the QM
> region. First, because there are steps (as I mentioned in the other e-mail)
> that are usually done with the system full-MM. Specifically, the initial
> energy minimization and thermalization.
>
> Secondly, there are QM/MM interactions that use MM parameters: the vdW
> interactions between QM-MM atoms utilizes the MM parameters for the QM
> atoms and, if your QM-MM border crosses bonds, any bond, angle or dihedral
> term involving at least one QM atom is calculated using the regular MM
> equations and parameters. So, the QM region does need MM parameters.
>
> Finally, I had the impression that your QM region is not a standard
> residue. So, for any of those parts, you would need to create the
> appropriate parameters for it.
>
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Recife - PE - Brasil
> +55-81-2126-7450 x5023
> > ---------- Forwarded message ----------
> > From: Gustavo Seabra
> > Date: 14 November 2012 12:40
> > Subject: Re: [AMBER] Problem with running QM/MM - MD simulation using
> AM1/d-
> > PhoT method in AMBER12
> > To: AMBER Mailing List
> >
> >
> > Hi Vojtech,
> >
> > Just to eliminate possibilities: Have you tried a different QM
> hamiltonian?
> > Does the same thing happen?
> >
> > Anyways, how did you parametrize the QM region?
> >
> > What I usually do when running QM/MM calculations is to first energy-
> > minimise the system, then slowly heat it to the desired temperature, all
> > with full-MM. Only after the system is reasonably thermalised at the
> final
> > temperature I turn on the QM region.
> >
> > Cheers,
> > Gustavo Seabra
> >
> >
> >
> >
> >
> > On Wed Nov 14 2012 08:05:29 Vojtech said:
> >> Dear all,
> >>
> >> I would like to mention here one strange issue that I have recently
> >> encountered in AMBER12.
> >>
> >>
> >>
> >> I try to run QM/MM MD simulation using recently implemented SE - AM1/d-
> > PhoT
> >> method (abbreviation AM1/d) as the qm_theory for the QM part of
> molecule.
> >> The system is RNA-enzym (Ribozyme) and contains just NA-nucleobases, Na+
> >> counter-ions and rectangular box of TIP3P molecules (around 30.000 atoms
> > in
> >> total). The QM region contains just one phosphate with the ribose-ring
> at
> >> one site, methoxy group on the other and 2 nucleobases within H-bond
> >> distance from both non-bridging oxygens of that phosphate (typically 49
> >> atoms). The link atoms are thereby placed instead of C-C bonds (or C-N
> > bonds
> >> in case of nucleobases).
> >>
> >> Problem is that my QM region suddenly 'explodes' during initial
> (typically
> >> 50 ps-long) heating phase (constant volume, example of script at the
> end)
> > as
> >> soon as the temperature of the system reaches ~250 K. Firstly hydrogen
> > atoms
> >> and them the other QM atoms just fly apart. I have also tried different
> >> modifications of my input script, charmm parameters and charges
> > (converting
> >> starting pdb to charmm psf file, then backwards using chamber module),
> > more
> >> sequentional pre-heating with some equilibration steps and even larger
> QM
> >> regions. All modifications resulted in same error during pre-heating or
> > just
> >> at the beginning of subsequent equilibration. Notably, initial QM
> >> minimalization fails (SCF convergency) for the system with largest QM
> > region
> >> (100 atoms). I have also tried to heat the system up to 200 K only and
> >> thereby it 'survises' the pre-heating phase. But during the
> equilibration
> >> phase (constant pressure) same issue occurs (also suddenly, there is no
> > hint
> >> of something going wrong / any possible trend in both QM/Total Energies
> ..
> >>
> >>
> >>
> >>
> >> I am very confused and will much appreciate any reply or suggestion.
> >>
> >> Thanks in advance,
> >> Vojtech
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 14 2012 - 12:00:03 PST
