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

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 17:48:41 CEST 2013



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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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