Thanks. Yes, like you guessed I used ntt=3, gamma_ln =2, but I tried
different initial configurations. I wonder if the problem can be solved by
adding counter ions to neutralize the system charge.
On Thu, Jun 6, 2013 at 3:22 PM, Brian Radak <radak004.umn.edu> wrote:
> >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.
> > > > _______________________________________________
> > > > 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
> > >
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 06 2013 - 14:30:12 PDT
