Carlos,
sander will have identical functions as pbsa, after the updates before
the deadline.
By the way, it turns out that the difference between pbsa and delphi is
due to delphi's slower convergence with respect to grid spacing. When I
use the 0.25 A grid spacing, the difference is within 1%.
Best,
Ray
Carlos Simmerling wrote:
> Ray,
> is pbsa going to continue being a separate program or can sander have
> those features? We'd like to use the pbsa updates in sander for things
> like hybrid solvent remd and so on.
> thanks
> Carlos
>
> Ray Luo wrote:
>
>> 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
