Re: amber-developers: Amber9 feature freeze coming soon...

From: David A. Case <>
Date: Tue, 13 Dec 2005 15:44:26 -0700

On Tue, Nov 22, 2005, David A. Case wrote:
> As I said in a previous e-mail, I would like to have the "feature
freeze" for
> Amber 9 in about two weeks.

Some of you may have noticed that I have let this deadline slip some. :-)

I have talked with most of you about where things stand, and my current
is to freeze the code on Dec. 23. After that, we need to concentrate on
running real applications (not just test cases) to make sure we are
reasonable results; (b) adding more sanity checks to the input, to try to
off bad simulations; (c) work on the Users' Manual, especially on the
in the "using sander for ...." chapter.

Here is an update on what I know about, quoting my earlier note from three
weeks ago:

> 1. update to pbsa, (not sure what changes are coming) -- Ray

...done...thanks, ray!

> 2. cleanup of multisander, removing -DREM flags, examples -- Carlos
> 3. incorporation of LES functionality into egb() -- Carlos

Carlos says he is close...

> 4. finishing serial capability for AMOEBA, + example -- Tom D.

This looks almost done...the first two amoeba test cases have been added,
and more are coming soon.

> 5. new divcon code (standalone + library) -- Bing, Seth, Kennie

The standalone I know is working; I haven't tested the library+ sander
yet, but I gather(?) from the CVS logs that this is nearing completion.

> 6. SCC-DFTB with correct gradients, etc. -- Gustavo, Adrian

This looks like it is working for vacuum like simulations. Ross will
Florida next week to get DFTB integrated for periodic simulations and for
GB. As time permits, he may also work with the divcon people to iron out
any problems in that part of the code.

> 7. support for binary trajectory (netcdf) files -- John, Tom C.

Carlos will send John the info needed in the traj file for REM
still need some ptraj code for this aspect.

> 8. folding into ptraj of clustering codes -- Tom C.
> 9. any new force-field files(?) Rob, Yong, Ray

Ray will be putting in a test case designed to ensure that the united atom
force field is working properly; others may want to add force-field
tests. Carlos sent me privately the "e16" mods to ff99; should these go
the amber9 tree (as a frcmod file)?

> 10. move EVB into force, have it work with PIMD -- Kim, Wei

I think this is close; the key point for me is to have the simple EVB code
really working; adding different coupling models should only come once we
sure the basic code is sound.

> 11. centroid dynamics(?) -- Francesco
> 12. PSF to prmtop converter(?) -- Tom C.

13. Wei and Ross have implemented the QMMM/PIMD connection. Wei is
on rewriting NEB so that it uses the same ideas as PIMD (and can use
as a way of generating the prmtop files).

But we do have to bring all this to a stopping point, so that we can get
full months of testing in without having to delay the release date.
e-mail me if you cannot make the Dec. 23 deadline, and I would greatly
that you not wait until the last minute to finish your changes.

Received on Wed Apr 05 2006 - 23:49:46 PDT
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