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 <jalem...@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
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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