[gmx-users] trjconv and "Floating point exception"
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
>> Looks like a corruption in the trajectory. What does gmxcheck say about
> 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 A. Lemkul, Ph.D.
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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