[gmx-users] Errors from alchemical_analysis.py from analyzing .xvg files

Nathan K Houtz nhoutz at purdue.edu
Wed Dec 16 04:35:51 CET 2015


This request is related to python programs used for analyzing gromacs outputs, not gromacs itself. If there is a more appropriate forum for this question, let me know and I apologize for posting here.

I have performed a bunch of thermodynamic-integration simulations for liquid water in Gromacs, and am trying to analyze the .xvg files with the python script mentioned in the ethanol solvation tutorial: http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy (I think the tutorial is out of date - the python script is now called alchemical_analysis.py and I think it is called with slightly different flags). It may be relevant that I'm using Windows 10 and installed Anaconda2 (64 bit) with the gui installer and then pymbar through Anaconda2 before downloading alchemical-analysis-master.

In a Windows command prompt, I entered:

>python alchemical_analysis.py -d C:\<xvg_directory>\ -t 200 -p 1 -v  > results

This is the result:

Traceback (most recent call last):
  File "alchemical_analysis.py", line 1224, in <module>
  File "alchemical_analysis.py", line 1166, in main
    nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
  File "C:\<...>\alchemical-analysis-master\alchemical_analysis\parser_gromacs.py", line 187, in readDataGromacs
    fs = sorted(fs, key=F.sortedHelper)
  File "C:\<...>\alchemical-analysis-master\alchemical_analysis\parser_gromacs.py", line 48, in sortedHelper
    self.state = l[0] = int(l[0]) # Will be of use for selective MBAR analysis.
IndexError: list index out of range

where <...> is just the directory to which I downloaded alchemical-analysis-master. I don't understand the error and cannot find help for it online. In the directory where I have the .xvg files, all the files are simply named integers: 0.xvg, 1.xvg, 2.xvg, .... 20.xvg, and there are no other files in that folder. I don't want to tinker with the python code and accidentally mess something up. Am I calling the script correctly? Could it be the operating system (Windows vs. Linux)? I might be able to get on a Linux machine if it would help.

Thanks very much,

N. H.

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