>From what you are saying it seems to me that your chosen QM/MM model and
system appear to have relative pKas contrary to your chemical intuition.
This is generally a non-starter for simulation.
In order to prevent transfer you would probably have to bias your sampling,
although, depending on how you wish to interpret your results this would
essentially be an arbitrary modification of PM6 and, not, not necessarily
easy to justify without at least some validation.
It could also be possible that your simulation is unstable due to a poor
starting structure or excessive thermostat noise (I assume you are using
ntt=3, gamma_ln > 0?). Semi-empirical methods are very Tolstoyan when it
comes to bad starting structures ("Each is unhappy in its own way"). Maybe
PM3 would display the same behavior with a different initial structure?
Brian
On Thu, Jun 6, 2013 at 2:55 PM, me, Nancy <bwan0408.gmail.com> wrote:
> I was just running normal NPT QM/MM dynamics without any biased sampling. I
> used the same initial configurations and velocities. The only difference is
> the QM theory. The hydrogen exchange on the hydroxyl group with hydronium
> hydrogen happened very fast with PM6, which is not likely it should be.
>
>
> On Thu, Jun 6, 2013 at 2:34 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > This is probably not a bug and can probably not be avoided without
> changing
> > your simulation protocol.
> >
> > PM3 and PM6 are quite different model quantum chemistries and there is no
> > reason to believe their behavior should be qualitatively identical (it
> goes
> > without saying that they will be quantitatively different). I doubt that
> > this "exotic" behavior with PM6 is due to an error in its implementation.
> >
> > Such a difference is likely either a natural "error" of the model
> > (*i.e.*predicted behavior that is not physically accurate) or else an
> > artifact of
> > your simulation protocol (*i.e. *some stochastic element of the sampling
> > protocol has caused the samples to diverge). Can you describe more what
> > your simulation protocol is?
> >
> > With *any* semi-empirical quantum method, it is probably a good idea to
> > validate by comparing to a respectable level of *ab initio* theory. It is
> > of course up to you and a referee as to what is compared. In this case I
> > would look at proton affinities, but that is just my opinion.
> >
> > Regards,
> > Brian
> >
> >
> > On Thu, Jun 6, 2013 at 2:11 PM, me, Nancy <bwan0408.gmail.com> wrote:
> >
> > > I am running a QM/MM simulation for the system that contains a hexose
> > > molecule, a hydronium molecule and water molecules. The hexose and
> > > hydronium molecules are in the QM region and water molecules are in the
> > MM
> > > region. When I run it with PM6, I found there is hydrogen atom exchange
> > > between that on hydroxyl groups of hexose and on hydronium molecule,
> but
> > > when I run the system with PM3, there is no hydrogen atom. I wonder if
> > this
> > > is a bug in PM6. Is there any way to avoid the hydrogen exchange using
> > PM6?
> > > Thanks.
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> >
> >
> >
> > --
> > ================================ 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.
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--
================================ 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.
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Received on Thu Jun 06 2013 - 12:30:03 PDT
