[gmx-users] jalemkul at vt.edu

vidhya sankar scvsankar_agr at yahoo.com
Sun Jun 17 16:31:10 CEST 2012

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  

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 


Thanks in advance 
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