Just a quick summary of this QM/MM problem and a bug fix.
The problem only occurs when qmshake=0; if noshakemask is used and
overlaps with iqmatoms (or qmmask), the number of degrees of freedom
"released" from this overlapped region will be count twice
technically.
So the fix includes,
for general QM/MM simulations:
1) if qmshake=0, and noshakemask is on, count the overlapped degrees
of freedom (if any), and subtract it from the total number of degrees
of freedom;
2) issue an error message when qmshake>0, but there are QM atoms
belongs to noshakemask;
for QM/MM TI simulations:
3) when qmshake=0, check the total number of the non-shaked atoms, see
whether or not they match in two simulations. If not, issue an error
message that suggests using noshakemask to match the noshake region.
Brian, the bonded terms with the proton are kept after reading your email.
Best,
Qiantao
On Mon, Sep 26, 2011 at 9:05 AM, Brian Radak <radak004.umn.edu> wrote:
> 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
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Received on Wed Sep 28 2011 - 13:30:02 PDT
