[gmx-developers] Re: Bug 597 and previous diff: any hint to a confused gromacs source code newbie?

ms devicerandom at gmail.com
Thu Nov 11 22:03:01 CET 2010

Hi, thanks for your quick reply,

On 11/11/10 20:52, Shirts, Michael (mrs5pt) wrote:
> My understanding is that the 4.5.x code has corrected this error
> independently from my commit.  So what is in the master now is correct.So
> I assume your question is how to backport the fix into 4.0.7?  Someone
> correct me if am wrong in either of these assumptions.

Uh, both by checking on git and by what Mark Abraham and other people 
said in the bugzilla, it seems that the relevant code in 4.0.7 (4.0.5 
actually, my fault) is the same than in 4.5:

"------- Comment #3 From M. Sandal 2010-10-19 12:34:20 CET [reply] -------

To understand if the problem I am encountering is related to this bug: 
Is the
code functionally the same in 4.0.7 ?

------- Comment #4 From Mark Abraham 2010-10-19 12:55:12 CET [reply] -------

Yes, Massimo - 4.0.7 and git release-4-5-patches are the same in this 
My theory is that at least some of the symptoms you are observing are 
on what I think is wrong code."

Am I wrong?

> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>> From: ms<devicerandom at gmail.com>
>> Date: Thu, 11 Nov 2010 14:59:19 -0500
>> To: "gmx-developers at gromacs.org"<gmx-developers at gromacs.org>
>> Cc: "michael.shirts at virginia.edu"<michael.shirts at virginia.edu>
>> Subject: Bug 597 and previous diff: any hint to a confused gromacs source code
>> newbie?
>> Hi,
>> I have to correct bug 597. To understand if and why, the bugzilla thread
>> and the thread on the users mailing list:
>> http://lists.gromacs.org/pipermail/gmx-users/2010-October/054950.html
>> can help :)
>> Now, I am trying to make sense of it, but before I noticed that Michael
>> Shirts has indeed already tried to fix the code. However the commit was
>> part of a huge "mistake" commit from a personal branch, as evidenced in
>> this mail:
>> http://lists.gromacs.org/pipermail/gmx-developers/2010-January/003884.html
>> Now, what I can't make sense of, are:
>> 1)Is that patch fine to fix bug 597?
>> 2)Is it enough for me to gather from that commit the dihres.c and
>> possibly the (new) functions it calls, and go from there, or is there
>> someone (possibly the author) who can explain me what are also the
>> relevant parts to patch? It seems to me that it changes quite a lot in
>> the file and I don't think I understand it all.
>> Thanks a lot. While I am an acquainted Python programmer, I have little
>> C experience and none with Gromacs source, so bear with me!
>> Yours truly,
>> Massimo
>> --
>> Massimo Sandal, Ph.D.
>> http://devicerandom.org

Massimo Sandal, Ph.D.

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