Dave,
I've updated my local amber9/pbsa code, and am in the process of testing
pbsa against delphi. I found two cases that the difference between the
two is larger than 1%. I'm looking into these right now. I think I can
meet the deadline in checking all features in pbsa: new Coulombic
energy, new pbradii, and new nonpolar/SA solvent. All are with test
cases and tutorials.
All the best,
Ray
David A. Case wrote:
>Hello to all:
>
>As I said in a previous e-mail, I would like to have the "feature freeze"
for
>Amber 9 in about two weeks. But please don't rush in to commit brand new
or
>untested code. We can issue patches or updates later if needed.
>
>Here is a list of some major things I hope we can get accomplished. I
would
>appreciate it if the people listed below could contact me (either on this
list
>or privately) to let me know where things stand:
>
>1. update to pbsa, (not sure what changes are coming) -- Ray
>
>2. cleanup of multisander, removing -DREM flags, examples -- Carlos
>
>3. incorporation of LES functionality into egb() -- Carlos
>
>4. finishing serial capability for AMOEBA, + example -- Tom D.
>
>5. new divcon code (standalone + library) -- Bing, Seth, Kennie
>
>6. SCC-DFTB with correct gradients, etc. -- Gustavo, Adrian
>
>7. support for binary trajectory (netcdf) files -- John, Tom C.
>
>8. folding into ptraj of clustering codes -- Tom C.
>
>9. any new force-field files(?) Rob, Yong, Ray
>
>10. move EVB into force, have it work with PIMD -- Kim, Wei
>
>11. centroid dynamics(?) -- Francesco
>
>12. PSF to prmtop converter(?) -- Tom C.
>
>We certainly don't have to have everything listed above. And thanks to
all
>who have been working at these tasks, plus those working on any I haven't
>mentioned....We've been making real progress in several areas:
>
>antechamber improvements (Junmei); parallel PIMD (Wei); big speed
improvements
>for periodic QM/MM (Mike, Ross); under-the-hood stuff for psander (Mike);
>code cleanup (Mike, DAC); updates to the manual (several people).
>
>...regards to all....dac
>
>.
>
>
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
Received on Wed Apr 05 2006 - 23:49:47 PDT
