You should file an issue on the alchemical-analysis issue tracker. https://github.com/MobleyLab/alchemical-analysis
On Tue, Dec 15, 2015 at 8:35 PM, Nathan K Houtz <nho...@purdue.edu> wrote: > Hello, > > > 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 (I think the tutorial is out of date - the python script is now called 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> > main() > 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. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
