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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>> 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.
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Received on Wed Sep 21 2011 - 07:00:03 PDT
