Dear Users: I'm having difficulty running MBAR after some free energy calculations (MBAR via alchemical-gromacs.py obtained from alchemistry.org). The input options to alchemical-gromacs.py have obviously changed since the site at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy was updated, but I've taken a look at the python source and it seems as if my invocation below should work. Nevertheless, I get an "Illegal instruction" error (See below).
gpc-logindm02-$ ls ANALYSIS/ ethanol.0.dhdl.xvg ethanol.2.dhdl.xvg ethanol.4.dhdl.xvg ethanol.6.dhdl.xvg ethanol.8.dhdl.xvg ethanol.1.dhdl.xvg ethanol.3.dhdl.xvg ethanol.5.dhdl.xvg ethanol.7.dhdl.xvg gpc-logindm02-$ python /project/p/pomes/cneale/GPC/exe/pymbar/trunk/examples/alchemical-free-energy/alchemical-gromacs.py -d ANALYSIS -p ethanol. -t 300 -s 1000 -v Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data. Started on Thu Sep 26 22:32:05 2013 Illegal instruction (omitting the -t -s and -v flags yields the same error). I realize that I'm hijacking the gromacs list a little bit here but there is no mailing list for http://www.alchemistry.org/ and it seems like a good idea to have these Q&A's archived. Thank you, Chris. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
