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MobleyLab / alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations
MIT License
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Lambda index out of bounds when accumulating free energies #70

Closed driesvr closed 8 years ago

driesvr commented 8 years ago

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 commented 8 years ago

Thanks. I'm guessing this is somewhat related to https://github.com/MobleyLab/alchemical-analysis/issues/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 notifications@github.com 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

— Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/70.

David Mobley Associate Professor Department of Pharmaceutical Sciences Department of Chemistry 3134B Natural Sciences I University of California, Irvine Irvine, CA 92697 dmobley@uci.edu work (949) 824-6383 cell (949) 385-2436

davidlmobley commented 8 years ago

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

davidlmobley commented 8 years ago

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 commented 8 years ago

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.