[gmx-developers] Gromacs 4.0.5 released?

[Justin A. Lemkul]

David Mobley wrote:
> Just to offer up my two cents on part of this:
>>>
>>> Sorry, we'll announce it :-) Actually, this was mostly a fix for a 
>>> powerpc build in Barcelona and rather than doing a separate build I 
>>> figured I could pack what we had in the release branch for everybody.
>>> In the future, I would probably prefer to move to a setup where we 
>>> semi-automatically release a new version from the release branch 
>>> every 2-3 weeks (together with nightly builds). Every time we 
>>> formally "prepare" for a release there ends up being "just one more 
>>> fix" that should go in - two days later the first person doesn't have 
>>> time to make the release, and then we wait another week, after which 
>>> there is "just one more fix", etc. ;-)
>>
>> Would such frequent releases cause problems with version consistency? 
>>  I always try to conduct my projects using the latest version of 
>> Gromacs (which is always recommended to make use of bug fixes and new 
>> features), but if we have new versions every few weeks, are users then 
>> encouraged to continue existing simulations under newer versions? 
>>  Certainly moving from 3.3.x to 4.0.x wouldn't make much sense, with 
>> all the lovely 4.0 features that are new; I'm referring mostly to 
>> minor revisions within the 4.0.x series.
>>
> 
> My take on this is that (a) frequent releases are good, because this 
> will allow people to use a version that incorporates known bugfixes. In 
> previous versions sometimes there have been many bugfixes floating 
> around that one would need to apply to have a bug-free code to run. But 
> (b) a particular project should always be done with ONE particular 
> version of GROMACS (either a particular point release, a particular CVS 
> branch & checkout date, etc.), with no switching in the middle, except 
> under exceptional circumstances. The idea should be that we provide 
> enough information in our papers that another group can reproduce our 
> calculations; this includes specifying what version of the code was used 
> for all calculations, which is a lot more difficult if one switches 
> codes during a project.
> 
> 

Thanks for the comments.  I agree that switching versions is a bad idea; I just 
didn't know if bug fixes pre-empted that thought.  I suppose it would only in an 
extreme case, but the simulations should probably be started over in that case, 
anyway.

The main reason I ask is that I took some flak in a recent manuscript review for 
using GMX-3.3; the project was started over 2 years ago, and that was the 
version available to us on the cluster at the time.  The complaint was that 
GMX-4.0 is "better" and "more reliable."  With even more rapid development, I'm 
just hoping I won't get picked on so much for minor version differences, since 
all of the new versions will be "better" and "more reliable," ideally :)

Hopefully my comments were not taken as a complaint; I am very grateful to the 
dedicated developers for their constant work and continued attention to 
improvements!

-Justin

> 
>> Also, there has been increasing discussion of this bug affecting more 
>> and more users:
>>
>> http://bugzilla.gromacs.org/show_bug.cgi?id=313
>>
>> Has anyone nailed down the source?  It seems that LJ-14 energies are 
>> not calculated correctly in 4.0.4, which seems pretty serious to me.
>>
>> Thanks in advance for any comments.
>>
>> -Justin
>>
>>> Cheers,
>>> Erik
>>> On May 12, 2009, at 12:47 PM, Manuel Prinz wrote:
>>>> Hi everyone,
>>>>
>>>> since last Saturday there's a gromacs-4.0.5.tar.gz available on the FTP
>>>> server. Nevertheless, I did not find an announcement on either the 
>>>> website
>>>> or the mailing list. Is this an official release tarball?
>>>>
>>>> On an aside, do you have plans to reactivate the announce mailing 
>>>> list? It
>>>> seems like it hasn't been used in years but I'd really appreciate it to
>>>> use it since announce emails can get lost in the regular list traffic
>>>> quite easily.
>>>>
>>>> All the best, and thanks for this great piece of software!
>>>>
>>>> Manuel
>>>>
>>>>
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>>> ------------
>>> Erik Lindahl   <lindahl at cbr.su.se>  Backup: <erik.lindahl at gmail.com>
>>> Associate Professor, Computational Structural Biology
>>> Center for Biomembrane Research, Dept. Biochemistry & Biophysics
>>> Stockholm University, SE-106 91 Stockholm, Sweden
>>> Tel: +46(0)8164675  Mobile: +46(0)703844534  Fax: mail a PDF instead
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>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================