Re: amber-developers: updated "to-do" list for amber8

From: David A. Case <>
Date: Fri, 14 Nov 2003 12:29:30 -0700

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
> at some point in time; Tom D. and I have not really discussed this, but
> 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
parameterization and potentials will be really useful. Tom D. is working
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
hard to justify putting any signficant effort right now into incorporating
current polarizable models into PMEMD. I should figure out a way to come
North Carolina for a visit so that all of us could have a detailed
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
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
machine-specific constants that are needed. Basically, make variables
the C-shell environment variables that were used before, and there is only
script ("configure") to maintain, rather than a dozen or more Machine.*
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.]


David A. Case                     |  e-mail:
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:                   
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Received on Wed Apr 05 2006 - 23:50:07 PDT
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