On Mon, May 9, 2011 at 4:38 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, May 09, 2011, B. Lachele Foley wrote:
> >
> > I tested tleap with 1-4 scaling on a fresh git pull on Friday. I
> > compiled AT and amber with and without the changes and ran tests for
> > AmberTools and Amber serial on both. The only test that behaved
> > differently after the changes is titled "check tprmtop1.dif", which
> > failed for legitimate reasons (the prmtop changed).
>
> Thanks!
>
> >
> > I think this is our first time changing actual code, so be duly warned.
> > I'll (try to) push the changes in a few minutes. It'll take me a day or
> > two more to generate and test patches for 1.4 and 1.5.
>
> I don't see a need for a 1.4 patch(?). First, this is really a new
> feature,
> although it can be argued that it is also a bugfix, since it is needed for
> certain types of calculations. I think it's OK then to add this as a 1.5
> bugfix, but it also seems quite reasonable to ask people that want this
> functionality to upgrade to 1.5; hence no need for a 1.4 bugfix.
>
I think we're probably always going to tell users to upgrade, anyway, since
AT15 works with Amber11, anyway (even if there are a few more steps), so my
vote falls to a 1.5-only patch as well.
>
> Note that, in general, feature enhancements should not be posted as
> bugfixes.
> Borderline cases will be considered on a case-by-case basis.
Related to this, there's a script that I had written to alter the intrinsic
PB radii of any prmtop to match whatever amber set the user chose so they
weren't locked into the one that was specified at startup. Normally I'd
hang on to this for the next release, but it would represent the only way to
create the mbondi3 radii set optimized for igb = 8 (the alternative of which
is to just use mbondi2, but that would get the salt bridges wrong compared
to the original parametrization).
The reason I didn't get it released with AmberTools 1.5 is because it wasn't
quite matching tleap's radii sets for DNA/RNA, and time is/was a hot
commodity. From my conversations with Carlos, I think he was interested in
making this a patch for AmberTools 1.5 to actually make the mbondi3 radii
accessible to non-developers (the script is in the developer tree). It
seems like it would make sense to release this prmtop util alongside a
tleap-enhancement if indeed we didn't want to just sit on it until AT12.04
(?). If there is interest in making this a bugfix, I'll get to it and fix
the issues with DNA/RNA to get it out. One possible reason to just sit on
it is that it won't be documented in the manual regardless (if people
actually read it for information). We could also just have it as a separate
download somewhere on the website as a compromise.
Thoughts?
Jason
> >
> > Do you want me to put a new top file in that test directory? I don't
> > mind, but also understand if someone else wants to inspect first.
>
> Go ahead and upgrade the test directory.
>
> ...thx...dave
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 09 2011 - 08:30:04 PDT
