problems with gromacs parser in alchemical-free-energy

[vvoelz]

We have found a problem in pymbar/examples/alchemical-free-energy/parsers/parser_gromacs.py with parsing large dhdl.xvg files. In slice_data(), there's a line:

f.len_first, f.len_last = (len(line.split()) for line in unixlike.tailPy(f.filename, 2))

the tailPy routine here is supposed to do a "tail" on the last two lines, and compare the number of fields; if they disagree, then the last line of the xvg file is corrupt and should be ignored.

In our case, we have found that unixlike.tailPy() gives incorrect results, truncating the last line. We suspect this may be because our xvg files have many alchemical intermediates (40 or more), all written in high-precision scientific notation, and unixlike.tailPy() has a character limit (?!)

def tailPy(f, nlines, LENB=1024): <------ ?

I think this could easily be fixed either rewriting unixlike.tailPy or just using the normal python read() or readlines(). --VInce

[jchodera]

@mrshirts: Can you guys take a look at this?

[kyleabeauchamp]

I think there is an outstanding pull request already waiting for review. We should see if that fixes the problem.

On 4/18/15, John Chodera notifications@github.com wrote:

@mrshirts: Can you guys take a look at this?

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Reply to this email directly or view it on GitHub: https://github.com/choderalab/pymbar/issues/181#issuecomment-94174240

[mrshirts]

I emailed pavel (who wrote the code) to take a look at it.

On Sat, Apr 18, 2015 at 12:57 PM, Kyle Beauchamp notifications@github.com wrote:

I think there is an outstanding pull request already waiting for review. We should see if that fixes the problem.

On 4/18/15, John Chodera notifications@github.com wrote:

@mrshirts: Can you guys take a look at this?

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Reply to this email directly or view it on GitHub: https://github.com/choderalab/pymbar/issues/181#issuecomment-94174240

— Reply to this email directly or view it on GitHub https://github.com/choderalab/pymbar/issues/181#issuecomment-94181011.

[kyleabeauchamp]

We still need someone to merge the pull request. I am not sufficiently familiar with the Gromacs code to review the changes.

[wesbarnett]

Hey I think the pull requests you mention were partly authored by me. Those were just a small fix to the graph output in the alchemical analysis script, not the actual gromacs parser, so I think this is a different issue.

[jchodera]

@mrshirts: Who has primary responsibility for the gromacs parser at this point?

[vvoelz]

@wesbarnett -- not to add more confusion, but are you referring to an output problem where the "vdWaals" free energy is always zero? This is something we consistently get.

--- Coulomb: 654.143 +- 5.676 643.565 +- 6.049 35.005 +- 0.171 9.977 +- 0.165 21.819 +- 0.128 18.144 +- 0.293 vdWaals: 0.000 +- 5.676 0.000 +- 6.049 0.000 +- 0.000 0.000 +- 0.000 0.000 +- 0.000 0.000 +- 0.000 TOTAL: 654.143 +- 8.027 643.565 +- 8.554 35.005 +- 0.171 9.977 +- 0.165 21.819 +- 0.128 18.144 +- 0.293

[wesbarnett]

@vvoelz Yes, that's one of the fixes in the pull request.

[mrshirts]

Who has primary responsibility for the gromacs parser at this point?

I don't think we've entirely decided. Pavel, would you be able do the maintenance for now?

[davidlmobley]

Pavel should be handling this. I'm talking with him today. Sorry for the delay here. We're new to GitHub and I was not monitoring issues on here until now. @wesbarnett - worlds collide. :)

[davidlmobley]

@FEPanalysis (Pavel) and I talked. He is working through issue #179 and #180 and may need test data from @wesbarnett. He also needs permissions to handle merging of pull requests (or we need to appoint someone else who will do it) and we're (@mrshirts @jchodera) sorting that out via e-mail now.

He also has a fix to @vvoelz 's issue #181 and will submit it as a pull request once it's sorted out who is handling merges.

[davidlmobley]

@vvoelz - we think this is resolved by https://github.com/MobleyLab/alchemical-analysis/pull/11. Can you check that it fixes your issue?