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

[Justin Lemkul]

On 9/23/13 11:39 AM, Dr. Vitaly Chaban wrote:
> 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.
>
>

All available evidence then suggests you have a corrupted frame about a third of 
the way through the trajectory.

-Justin

-- 
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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

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