noshakemask = ':1' was used to prevent a sander bomb because the TI code
requires that the shakemask in the two inputs be the same (and of course
shaking the proton in only one input is not an option as you quickly get
vlimit errors :P ) Is there a "more correct" way to not shake that OH bond?
Does this difference in degrees of freedom have any bearing on the dynamics
or is it just a quirk of the output?
The other error experienced in our group was not related to TI and was
determined to be an error in leap (she is still deciding if it is a user
error or a bug).
On Fri, Sep 23, 2011 at 3:25 PM, Qiantao Wang <qiantao.wang.gmail.com>wrote:
> 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
> >>
> >
>
> _______________________________________________
> 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.
_______________________________________________
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Received on Fri Sep 23 2011 - 13:30:02 PDT
