[gmx-users] About Mike Harms python script

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 17 01:08:01 CEST 2012

On 6/16/12 11:49 AM, vidhya sankar wrote:
> Dear justin  Thank you for your previous reply
>                    I am doing  Umbrella sampling in gromacs
> I have 30 set of initial configuration in .gro file format .Now i would like to
> do NPT equilibration and  umbrella sampling for all these configuration (for
> these i have to carry out 30 times equilibration and 30 times umbrella
> sampling)  to  Automate these process i used the python script provided by Mike
> Harms. but when invoke the 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
> Traceback (most recent call last):
>    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  have all the required files ( index.ndx files , dist.xvg files, , .gro files
> and .mdp files) in the  running directory

Based on the error message, it would seem that your dist.xvg file doesn't have 
anything in it.  What does it contain?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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