[gmx-users] Continuing a FEP alchemical

[Alex]

Dear Hannes,

Yes, I mean David Mobley's tool.
I checked it out, however it crashed exactly in the *.xvg file (prd.15.xvg
and afterward) in which additional \lambada getting involved. I invoked
below command to get rid of other method except TI:

"alchemical_analysis -p prd. -u kcal -f 20 -o 100dis -s 100 -c -g -v -m
'-ti_cubic-dexp-iexp-bar-mbar' -i 10",


Traceback (most recent call last):
  File "/usr/bin/alchemical_analysis", line 9, in <module>
    load_entry_point('alchemical-analysis==1.0.2.dev0', 'console_scripts',
'alchemical_analysis')()
  File "/usr/lib/python2.7/site-packages/alchemical_analysis-
1.0.2.dev0-py2.7.egg/alchemical_analysis/alchemical_analysis.py", line
1207, in main
    nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
  File "/usr/lib/python2.7/site-packages/alchemical_analysis-
1.0.2.dev0-py2.7.egg/alchemical_analysis/parser_gromacs.py", line 308, in
readDataGromacs
    nsnapshots[nf,nf] += unixlike.wcPy(f.filename) - f.skip_lines -
1*bLenConsistency
IndexError: index 15 is out of bounds for axis 1 with size 15

Thanks.

Best regards,
Alex


On Wed, Dec 28, 2016 at 5:38 PM, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk
> wrote:

> On Wed, 28 Dec 2016 17:24:08 +0100
> Alex <alexanderwien2k at gmail.com> wrote:
>
> > Thank for your response.
> >
> > You mean for the TI analysis, now problem if one .xvg file (e.g.
> > case.3.xvg) has just 15 columns while another .xvg file (e.g.
> > case.18.xvg) has 20 columns? and still the "alchemical analysis
> > package" could be used to calculate the free energy change via TI
> > method?
>
> I suppose you mean David Mobley's tool.  Yes, it can do that.  You can
> easily check that yourself though.
> --
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