[gmx-users] g_covar Segmentation fault problem

[gozde ergin]

Ok by using version 4.6.6 I got this segmentation fault error which means
number of frames should be equal or bigger than the number of degrees of
freedom.


On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/16/15 12:26 PM, gozde ergin wrote:
>
>> 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?
>>
>>
> Offhand, I don't know which outdated versions work and which don't.  To be
> safe:
>
> 4.6.x series, use version >= 4.6.6
> 5.0.x series, use version 5.0.5
> Any other version in the development repo (master, release-5-0, etc)
>
> -Justin
>
>
>
>>
>>
>>
>> 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
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> 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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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