[gmx-users] jalemkul at vt.edu

[Justin A. Lemkul]

On 6/17/12 10:31 AM, vidhya sankar wrote:
> Dear Justin Thank you for your previous reply
> How to solve error obtained when i invoke  command as follows
> ./setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh &> caught-output.txt
> I got error as follows in Caught_output .txt
>
> File "./setupUmbrella.py", line 182, in <module>
> out = main()
> File "./setupUmbrella.py", line 150, in main
> distance_table = readDistanceFile(distance_file)
> File "./setupUmbrella.py", line 49, in readDistanceFile
> value = float(columns[1])
> IndexError: list index out of range
>

I did not write the script.  Mike Harms' email is provided in the tutorial so 
you can contact him for bug reports and support requests.

> As you mailed me in previous mail  i  showed the dist.xvg file  also i have
> obtained this .xvg file through your Distance.pl script It contains as follows
> This file was created Sun Jun 17 19:23:40 2012
> # by the following command:
> # g_dist_d -s 0.154protopull.tpr -f conf143.gro -n index3.ndx -o dist143.xvg
> #
> # g_dist_d is part of G R O M A C S:
> #
> # Great Red Owns Many ACres of Sand
> #
> @    title "Distance"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Distance (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "|d|"
> @ s1 legend "d\sx\N"
> @ s2 legend "d\sy\N"
> @ s3 legend "d\sz\N"
>   143.0000000    0.5957624    0.0363277 -0.0382985    0.5934192
>
> Like above several dist file i have obtained  as dist25.xvg,  dist130.xvg,
> dist158.xvg Also i have one doubt What is the difference between .xvg file
> obtained by both  distance.pl script and g_dist tool Can i use the .xvg file
> obtained through g_dist command as summary_distance.dat by mere renaming .xvg file
>

There is no real difference, and the workflow was admittedly designed to be a 
bit awkward.  The reason is for instructional purposes - I wanted it to be 
absolutely clear the connection between each individual coordinate file and the 
COM distance in each of those frames.  What's more, the manner in which frames 
are written out separately is far more efficient than running g_dist to get the 
distances over time, then selectively run trjconv -dump to extract out however 
many specific frames you want.

-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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