Lambda index out of bounds when accumulating free energies

[driesvr]

Hi,

I'm getting the following error when I use alchemical-analysis for the second part of my run (bonded, LJ and masses).

File "/Users/dvr/Work/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 1226, in
main()
File "/Users/dvr/Work/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 1212, in main
totalEnergies()
File "/Users/dvr/Work/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 583, in totalEnergies
dF[name] += df_allk[k][name]
IndexError: index out of bounds

Everything works fine for the first and third part of the transformation with the same alchemical-analysis version and settings. Detailed output and input files can be found here:
https://www.dropbox.com/sh/vmjh7rmswbg0bd8/AADUpt8622PBUnxill6eOoIma?dl=0

Kind regards

Dries

[davidlmobley]

Thanks. I'm guessing this is somewhat related to
#65 in that we've
probably not tested this with the same number of or distribution of lambda
components that you're using. Hopefully the fix will be simple, though as
the other issue notes there are more long-range planning issues to deal
with.

Sorry for the delay here. I'm swamped in the first part of the week so it
may take me til late this week to get a look at it.

On Sun, Jan 24, 2016 at 4:10 AM, Dries VR [email protected] wrote:

Hi,

I'm getting the following error when I use alchemical-analysis for the
second part of my run (bonded, LJ and masses).

File
"/Users/dvr/Work/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py",
line 1226, in
main()
File
"/Users/dvr/Work/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py",
line 1212, in main
totalEnergies()
File
"/Users/dvr/Work/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py",
line 583, in totalEnergies
dF[name] += df_allk[k][name]
IndexError: index out of bounds

Everything works fine for the first and third part of the transformation
with the same alchemical-analysis version and settings. Detailed output and
input files can be found here:
https://www.dropbox.com/sh/vmjh7rmswbg0bd8/AADUpt8622PBUnxill6eOoIma?dl=0

Kind regards

Dries

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David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
[email protected]
work (949) 824-6383
cell (949) 385-2436

[davidlmobley]

Investigating this now. It could be it is also related to #64 .

[davidlmobley]

This should be resolved by #72 . Can you test that it works for you?

You may also want to read #65 , as there is a larger enhancement we need to make to make the code report the correct labels for different lambda components in cases where you're not doing just a simple consecutive Coulomb-then-van-der-Waals transformation, as you aren't here. But at least now things should work.

[driesvr]

Hi, just tested the patch and it looks like everything's working.
Thanks.

#65 looks like a very interesting enhancement, it would be nice to see the contribution of various terms.

As everything's working on my end, I'll go ahead and close this issue. I'd be happy to help if you require any further testing though.