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luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
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Analyzing incomplete runs #118

Open xy21hb opened 12 months ago

xy21hb commented 12 months ago

If some pairs are broken, could analyze_results.py still work, suppose e.g. if only FXR_12_FXR_88 pair of the tutorial is broken, e.g. system is unstable, only intermediate pdbs are written and gromacs fails to collect energy files. I wonder how to obtain the results from other pairs, considering the generated pertubation_map.

xy21hb commented 12 months ago

Error msg is below, some steps of structures are not stable, and GMX fails to collect edr energy files

image

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luancarvalhomartins commented 12 months ago

I'm theory, running with --no_checks should allow for such.

However, your error message suggests that there are some edr files in the rerun dir, which could cause errors anyway. Would you mind retrying with --no_checks, and, in case it doesn't work, post either the .tgz or the directory structure (should your data be sensitive)?

Thank you very much.

xy21hb commented 12 months ago

Though I have not checked the structure, I believe it is due to some unstable ligs since the system is a large membrane protein. Running with --no_checks would give the same error msg. So, to analyze incomplete runs, simply excluding those runs in pack.sh would work.

luancarvalhomartins commented 12 months ago

Ok, so --no_checks wasn't enough. Let me take a look at the code to fix this.

Thank you again for reporting.