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deGrootLab / pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
GNU Lesser General Public License v3.0
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ff libraries in develop are unchecked/untested (and likely problematic) #5

Open matteoaldeghi opened 6 years ago

matteoaldeghi commented 6 years ago

These ff libraries come from merging master (dna ff) and proline branches (protein ff), and then merging dna and protein forcefields so that they are in a single folder. It is likely the resulting libraries might be broken in some way or another. I have been using bits and pieces (either only protein, dna, or rna) of the amber forcefields for testing of refactored code, which seemed fine, but at some point for any real usage we should re-build the libraries from scratch, maybe after having implemented some automated energy tests/checks.

bisdan commented 10 months ago

Hello,

could we please get an update on this? Is it ok to use the force fields in develop for simulations involving only proteins? For example, "charmm36m-mut" does not seem to present in master (for proteins). On the other hand, if py3/Icolos support is required, one is directly forwarded to the develop branch.

Thanks in advance

I just noticed that you perform a few pytests in the develop branch which seem to pass. Here you specifically test "amber99sb-star-ildn-mut". Can this issue/warning be closed then?