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

ms devicerandom at gmail.com
Fri Nov 12 11:26:59 CET 2010

On 12/11/10 01:57, Mark Abraham wrote:
> On 12/11/2010 7:52 AM, 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.
> The code in src/gmxlib/dihres.c is unchanged from that of a year ago
> (master or release-4-5-patches), so I think this error is not fixed.

Yes, that's what looked like to me on the git web interface.

I also have another question: I actually copied the code snippet (well, 
I reimplemented it verbatim in Python) and I looked at the potential it 
generates -at a glance, it seems fully consistent with what is expected, 
a periodic flat-bottomed harmonic potential centered around phi0... so I 
am unsure of what is the bug.

> Mark
>> 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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