[gmx-users] jalemkul at vt.edu
Justin A. Lemkul
jalemkul at vt.edu
Sun Jun 17 16:38:54 CEST 2012
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)
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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