[gmx-users] g_covar Segmentation fault problem

gozde ergin gozdeeergin at gmail.com
Thu Jul 16 18:27:17 CEST 2015


Thank for reply Justin but I have difficulty to understand which version
has this bug?
If  'Segmentation fault because of #DOF and frames numbers difference' is a
bug than gromacs 4.6.3 is working correctly, right?





On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/16/15 10:22 AM, gozde ergin wrote:
>
>> Dear gromacs user,
>>
>> In order to estimate system absolute entropy value I want to use g_covar +
>> g_anaeig commands.
>>
>> However when I *'g_covar -f nvt.trr -s nvt.tpr'*  I get a segmentation
>> fault after *'Diagonalizing ....'* step from gromacs 4.6.6 and 5.0.3.
>>
>>
>>
>>
>>
>>
>>
>> *Constructing covariance matrix (12258x12258) ...Last frame       4000
>> time
>> 4000.000   Read 4001 framesTrace of the covariance matrix: 12454.6
>> (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation
>> fault (core dumped)*
>>
>> But the same command, executed with g_covar of gromacs 4.6.3 works without
>> any error or fault.
>>
>> Was it a bug and corrected for newer versions? I saw  the release note of
>> *
>> 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames
>> for a covariance analysis is fewer than the number of degrees of
>> freedom'  *for
>> gromacs 4.6.6.
>>
>>
> The bug was also fixed for 5.0.5.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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