[gmx-users] Floating point exception(core dumped) still happen when running a serial job

[Justin Lemkul]

On 6/20/15 11:04 AM, Zhang, Cheng wrote:
> Dear GROMACS expert,
>
> (Relevant files can be found at https://copy.com/7DMkn6OxJBqEZtqh)
>
>
> I still encountered error of "Floating point exception(core dumped)" when running "g_rms -s md_0_1.tpr -f md_0_1.xtc" on my Ubuntu. In the prompt, it stopped and showed the error when it came to 20 ns:
>
>
> ... ...
>
> Reading frame    1700 time 17000.000
>
> Reading frame    1800 time 18000.000
>
> Reading frame    1900 time 19000.000
>
> Reading frame    2000 time 20000.000
>
>
> However, in my another repeat simulation, it could successfully run "g_rms -s md_0_1.tpr -f md_0_1.xtc" based on another md_0_1.xtc file. So I think there is something wrong with this .xtc file. Could someone please help me identify the problem?
>

What does gmx check tell you about the contents of the problematic .xtc file? 
It's probably corrupted.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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