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

Wed Feb 19 03:11:14 CET 2014

Szilárd already activated it a couple of hours ago (just noticed he 
replied to me only). The issue is already submitted also. Thanks anyway.

Best,
Antonio

On Wed, 19 Feb 2014, Mark Abraham wrote:

> 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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