Unfortunately that is exactly what I *don't* want to do. The bonded terms
with the proton are necessary at the end point where it is completely out of
the QM region, although I suppose an appropriate extrapolation scheme from a
lambda value "very close" to that endpoint could be sufficient. I'm
essentially trying to implement the "dual topology single coordinate" method
from Qiang Cui's group:
Li, *et al.* J Phys Chem B 2003, 107, 8643.
Couldn't that solution also be implemented by creating a suitable prmtop, or
would that also encounter the degrees of freedom problem?
Brian
On Sun, Sep 25, 2011 at 9:26 AM, Qiantao Wang <qiantao.wang.gmail.com>wrote:
> I guess why we didn't see difference in kinetic energy is prabobaly
> because the energy was being synchronized in TI simulation. However,
> the temprature in output used the synchronized energy, but different
> degrees of freedom, thus we saw different temparture in two output. So
> I think it's parabobaly worth a while to making sure we have correct
> degrees of freedom in such simulations.
>
> What I am doing is, whenever the QM/MM boundary cross a QM-MM(H)
> hydrogen bond (and when qmshake=0, i.e. no shake applied to the QM
> region), we remove all the connectivities between the H atom and other
> bonded QM atoms, making it a free particle.
>
> Best,
> Qiantao
>
> On Sat, Sep 24, 2011 at 8:51 AM, case <case.biomaps.rutgers.edu> wrote:
> > On Fri, Sep 23, 2011, Brian Radak wrote:
> >>
> >> Does this difference in degrees of freedom have any bearing on the
> dynamics
> >> or is it just a quirk of the output?
> >
> > I would have thought that the thermostat would have been affected, and
> hence
> > the velocities on two sides. But if that happened, the kinetic energies
> would
> > not be equal, and very quickly the coordinates and potential energies
> would
> > not match. Since that is not happening, it looks like just a quirk in
> the
> > output.
> >
> > I must say that having an O-H bond cross the QM/MM boundary sounds very
> odd.
> > We certainly never looked at anything like this when developing or
> testing the
> > code. Let's see how Qiantao's fix works out.
> >
> > ...dac
> >
> >
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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 : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Mon Sep 26 2011 - 06:30:03 PDT
