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
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> radakb.biomaps.rutgers.edu
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Received on Thu Jun 06 2013 - 12:00:04 PDT
