[gmx-users] trjconv and "Floating point exception"

[Dr. Vitaly Chaban]

Dr. Vitaly V. Chaban


On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote:
>>
>> Using trjconv -f traj.xtc -o confout.gro -dump 15000000, I routinely
>> get the following error:
>>
>> Select a group: 0
>> Selected 0: 'System'
>> Reading frame       0 time    0.000
>> Precision of traj.xtc is 0.004 (nm)
>> Using output precision of 0.001 (nm)
>>
>> Back Off! I just backed up confout.gro to ./#confout.gro.1#
>> Reading frame   17000 time 5100000.000   Floating point exception (core
>> dumped)
>>
>
> Looks like a corruption in the trajectory.  What does gmxcheck say about
> traj.xtc?


gmxcheck -f traj.xtc

Reading frame     17000 time 5100000.000   Killed


>> Can you bypass the frame using -b and dump out the desired frame?


No. The process comes to 5.1 ms and is killed.






> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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