<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear justin Thank you for your previous reply<br></div><div> I am doing Umbrella sampling in gromacs <br></div><div>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 <span style="font-weight: bold;">(f</span>or 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 <font face="Arial"><font size="3">Mike Harms. but when invoke the command as follows</font></font></div><div><font face="Arial"><font size="3">.<span style="font-weight: bold;">/setupUmbrella.py summary_distances.dat 0.2 run-umbrella.sh
&> caught-output.txt</span></font></font></div><div><font face="Arial"><font size="3"><span style="font-weight: bold;">I got error as follows in Caught_output .txt</span><br></font></font></div><div><font face="Arial"><font size="3"><br></font></font></div><div style="font-weight: bold;"><font face="Arial"><font size="3">Traceback (most recent call last):<br> File "./setupUmbrella.py", line 182, in <module><br> out = main() <br> File "./setupUmbrella.py", line 150, in main<br> distance_table = readDistanceFile(distance_file)<br> File "./setupUmbrella.py", line 49, in readDistanceFile<br> value = float(columns[1])<br>IndexError: list index out of range</font></font></div><div><br></div><div><font face="Arial"><font size="3">I have all the required files ( index.ndx files , dist.xvg files, , .gro files and .mdp files) in the running
directory<br></font></font></div><div><font face="Arial"><font size="3">How to solve these error</font></font></div><div><font face="Arial"><font size="3">Thanks In advance<br></font></font></div><div></div></div></body></html>