One more thing. I think if you are using qmshake=0, then you may not
want to use noshakemask=':1' in the cntrl name list, since this will
double count the vibrational degree of freedom of hydrogen atoms in
the QM region (i.e. 4 more DOF in your case).
Best,
Qiantao
On Fri, Sep 23, 2011 at 3:08 PM, Qiantao Wang <qiantao.wang.gmail.com> wrote:
> Hi Brian,
>
> Some updates.
>
> In your file 1, the O-H bond is in the QM region. When qmshake=0,
> sander will exclude the O-H bond from the hbond list. However, in your
> file 2, the O-H bond cross the QM/MM boundary, so O is QM and H is MM.
> In this case, sander will include the O-H bond in the hbond list no
> matter qmshake=0 or not. This difference thus give a difference of 1
> in number of degrees of freedom between two simulations.
>
> I have a fix, but still under test. If you are interested, I can
> commit it to the york directory in the repositery sometime soon.
>
> Regarding the other problem (NPT simulation crashes) experienced in
> your group. Was it a TI calculation as well? If not, could you give
> more details about the problem please?
>
> Best,
> 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
>>> >>>
>>> >>>
>>> >>> _______________________________________________
>>> >>> 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 : 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
>>> >
>>>
>>> _______________________________________________
>>> 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 : 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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Received on Fri Sep 23 2011 - 12:30:05 PDT
