[gmx-users] system hangs while running perl distances.pl

[Justin Lemkul]

On 5/12/13 6:40 AM, Arunima Shilpi wrote:
> Respected Sir
>   many many thanks for your reply to my last mail. while running
>
> trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep
>
> I selected group 0 for the system...
>
> but while i run perl distances.pl
>
> it says processing file 236...and than the system hangs,,,,, no more
> blinking along the terminal... while when I run indivdual file for distance
> calculation i am able to run the command
>
> g_dist -s pull.tpr -f conf1.gro -n index.ndx -o dist1.xvg < groups.txt
>
> i request you to kindly guide me to debug the error
>

If the script any any Gromacs commands it calls run fine for 235 frames, there 
is no Gromacs-related reason that it should stop.  Try running the command 
yourself for the problematic frame and see if there is an issue.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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