Hi Brian,
Yes, I noticed that in MEO input, the HO atom is excluded from the QM
region. I suspect this is the cause of problem in number of degrees of
freedom.
However, what confused me is: I tried to do a similar QM to QM TI with
a NMA in a water box. When lambda=0, all 12 atoms of NMA are QM atoms;
when lambda=1, the H attached to N is excluded from QM region. The
number of degrees of freedom in this case are same in two files. And
the temperature are perfectly matched. This is why I'm now trying to
understand the code.
Thanks for the update.
Qiantao
On Wed, Sep 21, 2011 at 4:44 PM, Brian Radak <radak004.umn.edu> wrote:
> Hi Qiantao,
>
> That's very interesting. I should mention that in the second parm7, there
> is a proton with zero charge that is not part of the quantum region.
> Possibly related?
>
> Another person in our group has been experiencing a problem with different
> symptoms (NVT simulations work but NpT simulations crash). The conclusion
> was also that the number of degrees of freedom was being differently
> calculated in each.
>
> Brian
>
> On Wed, Sep 21, 2011 at 3:43 PM, Qiantao Wang <qiantao.wang.gmail.com>wrote:
>
>> Hi Brian,
>>
>> I think the problem you experienced has something to do with the way
>> that sander counts the number of degrees of freedom, on which
>> temperature calculation depends.
>>
>> Taking your input file as an example, ME input generates a N.D.F. of
>> 9397, but MEO input gives a N.D.F. of 9396. I think this difference is
>> the reason of a constant 0.03~0.04K difference in TEMP in your output.
>>
>> Now one thing I have not fully understood is the way of counting the
>> number of degrees of freedom in the code, so cannot give you a
>> solution yet. Trying to get a bugfix soon, hopefully.
>>
>> Thanks,
>> Qiantao
>>
>> On Wed, Sep 21, 2011 at 9:40 AM, Brian Radak <radak004.umn.edu> wrote:
>> > Sorry, attachments were too big, here are dropbox links instead:
>> >
>> > http://dl.dropbox.com/u/40984968/ME_NVT_0.50_1.inp
>> > http://dl.dropbox.com/u/40984968/MEO_NVT_0.50_1.inp
>> > http://dl.dropbox.com/u/40984968/ME_NpT_0.50_1.crd
>> > http://dl.dropbox.com/u/40984968/ME.parm7
>> > http://dl.dropbox.com/u/40984968/MEO.parm7
>> >
>> > On Wed, Sep 21, 2011 at 8:54 AM, Brian Radak <radak004.umn.edu> wrote:
>> >
>> >> Jason - It is possible that this is an older version of Amber 11. It is
>> >> the development code within our group, although I thought it safe to
>> assume
>> >> that all of the proper git updates had been performed.
>> >>
>> >> Qiantao and Prof. Case - Attached are some input files (.inp, .parm7,
>> and
>> >> .rst7/.crd) for one window of a TI simulation for the pKa of methanol.
>> Note
>> >> that this is a QM - QM TI where the system charge changes at the
>> endpoints
>> >> leaving an uncharged dummy proton in one.
>> >>
>> >> Brian
>> >>
>> >>
>> >> On Wed, Sep 21, 2011 at 7:52 AM, David A Case <case.biomaps.rutgers.edu
>> >wrote:
>> >>
>> >>> On Tue, Sep 20, 2011, Brian Radak wrote:
>> >>>
>> >>> > I encountered the same behavior with 1000 steps of ntt=0 and ntt=3 (I
>> >>> can't
>> >>> > imagine that more steps would suddenly make it better). Judging by
>> the
>> >>> fact
>> >>> > that all of the other fields are identical, I'm going to agree with
>> your
>> >>> > speculation of a computing error or else a rounding error in the
>> >>> printing.
>> >>>
>> >>> Brian: I think we should see your inputs, because something funny is
>> going
>> >>> on.
>> >>> My experience is to see perfect matches, including with the
>> temperature.
>> >>> But
>> >>> there are all kinds of ways in which your inputs might be different
>> than
>> >>> mine.
>> >>>
>> >>> ...thx...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
>> >> ====================================================================
>> >> Sorry for the multiple e-mail addresses, just use the institute
>> appropriate
>> >> address.
>> >>
>> >>
>> >
>> >
>> > --
>> > ================================ 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
>> > ====================================================================
>> > 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
>> >
>>
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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
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
> _______________________________________________
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Received on Wed Sep 21 2011 - 14:30:03 PDT
