[gmx-users] g_principal -- bug or very bad choice of filenames

[Mark Abraham]

It shows as active to me...

Mark


On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista <baptista at itqb.unl.pt>wrote:

> On Fri, 7 Feb 2014, Justin Lemkul wrote:
>
>
>>
>> On 2/7/14, 6:08 PM, Antonio Baptista wrote:
>>
>>> Dear all,
>>>
>>> This is a follow-up to an old thread on g_principal, which continues (as
>>> of
>>> version 4.6.5) to suffer from what I would call a bug or, at least, a
>>> very bad
>>> and misleading choice of output file names. This message is primarily a
>>> further
>>> warning to users, but I also hope that it promotes the solution of the
>>> problem
>>> (I explicitly indicate below the small required code changes).
>>>
>>> The program g_principal "calculates the three principal axes of inertia
>>> for a
>>> group of atoms" and generates three output files with the default names
>>> axis{1,2,3}.dat. Although the content of these files is not explained,
>>> their
>>> names naturally suggest that axisN.dat contains the xyz components of
>>> the Nth
>>> principal axis (presumably in the conventional major-to-minor order).
>>> Indeed,
>>> each of these files contains (besides the time) 3 real values per frame,
>>> and
>>> this interpretation also yields three vectors which are orthonormal, as
>>> one
>>> would expect for the new frame defining the principal axes.
>>>
>>> However, this "natural" interpretation is wrong, and not because of a
>>> different
>>> axes order. As correctly identified by Chris Neale in the message
>>> included
>>> below, the file axis1.dat contains the x components of the 1st, 2nd and
>>> 3rd
>>> axes, the file axis2.dat their y components, and the file axis3.dat
>>> their z
>>> components (he checked with VMD, we did it with in-house programs in C
>>> and
>>> Octave). I think this a rather convoluted and extremely misleading way
>>> to output
>>> the principal axes.
>>>
>>> My guess is that this problem derives from a simple confusion between
>>> the form
>>> of the orthogonal matrix obtained when solving the eigenvalue problem --
>>> depending on the adopted algorithm, the vectors defining the new basis
>>> (the
>>> principal axes) can be either the columns or the rows of this matrix. I
>>> didn't
>>> look beyond gmx_principal.c, but the problem can be easily solved there
>>> by
>>> replacing the current lines
>>>
>>>          fprintf(axis1, "%15.10f     %15.10f  %15.10f  %15.10f\n", t,
>>> axes[XX][XX], axes[YY][XX], axes[ZZ][XX]);
>>>          fprintf(axis2, "%15.10f     %15.10f  %15.10f  %15.10f\n", t,
>>> axes[XX][YY], axes[YY][YY], axes[ZZ][YY]);
>>>          fprintf(axis3, "%15.10f     %15.10f  %15.10f  %15.10f\n", t,
>>> axes[XX][ZZ], axes[YY][ZZ], axes[ZZ][ZZ]);
>>>
>>> with
>>>
>>>          fprintf(axis1, "%15.10f     %15.10f  %15.10f  %15.10f\n", t,
>>> axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
>>>          fprintf(axis2, "%15.10f     %15.10f  %15.10f  %15.10f\n", t,
>>> axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
>>>          fprintf(axis3, "%15.10f     %15.10f  %15.10f  %15.10f\n", t,
>>> axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
>>>
>>> With this change, the file names would make perfect sense, with
>>> axisN.dat simply
>>> containing the components of the Nth principal axis. (Note that both the
>>> by-row
>>> and by-column readings give orthonormal vectors, because this is an
>>> orthogonal
>>> matrix.)
>>>
>>> The file moi.dat also produced by g_principal is fine, containing the
>>> moments of
>>> inertia along the principal axes in the proper order (lowest to highest,
>>> since
>>> the inertia _around_ those axes increases as one goes from the major to
>>> the minor).
>>>
>>> I believe that, as it stands now, g_principal is misleading many users
>>> into the
>>> wrong interpretation of its output. Maybe some developer wants to have a
>>> look at
>>> this issue and introduce my suggested fix.
>>>
>>>
>> Please file an issue on redmine.gromacs.org with all of the above
>> information. Thanks for the thorough report!
>>
>
> More than a weak later, http://redmine.gromacs.org/login keeps telling me
> that "Your account was created and is now pending administrator approval."
> Is this normal? Or maybe I missed some email message...
>
> Best,
> Antonio
>
>
>
>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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