On Thu, Nov 13, 2003, Robert Duke wrote:
> I actually have two other cuts, done recently. One drops the
> non-CIT code paths (which mostly supported amber 6 style polarization
and a
> few little-used options), should we want to put polarizable ff code in
pmemd
> at some point in time; Tom D. and I have not really discussed this, but
it
> is a possibility that we could relatively quickly have polarizable ff's
in a
> pmemd version.
The "problem" with polarizable potentials is this: we are not really sure
what
parameterization and potentials will be really useful. Tom D. is working
on
implementing Jay Ponder's ideas, which have some overlap with what Amber
currently has, but a lot of important differences as well. So it's
probably
hard to justify putting any signficant effort right now into incorporating
our
current polarizable models into PMEMD. I should figure out a way to come
to
North Carolina for a visit so that all of us could have a detailed
discussion
of what is both possible and desirable in this area.
Cleaning up PMEMD by removing the non-cit stuff sounds good. Maybe this
should just go in to the amber8 release, rather than as a new web release.
My target date for the amber8 code freeze (other than bug fixes) is
Jan. 1, 2004.
[Another point/idea that I forgot to mention yesterday: Amber 8 no longer
has
MACHINE files and the "Compile" c-shell script. Rather, "configure"
creates a
config.h file that is included in lower-level Makefiles, and which defines
any
machine-specific constants that are needed. Basically, make variables
replace
the C-shell environment variables that were used before, and there is only
one
script ("configure") to maintain, rather than a dozen or more Machine.*
files.
I don't think it would be very hard to integrate this into what is already
there in PMEMD. Then "pmemd" could become a subdirectory under
amber8/src, as
for all of the other code. I may try this myself, since I will be playing
some with PMEMD over the next few weeks.]
.regards....dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Wed Apr 05 2006 - 23:50:07 PDT
