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
>
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Received on Wed Sep 21 2011 - 13:00:04 PDT
