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Gromacs compatibility #51

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EzryStIago opened this issue Oct 10, 2024 · 0 comments

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EzryStIago commented Oct 10, 2024 •

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The backend cannot currently handle Gromacs outputs.
To do:

check the extension of the fepout files - use either the namd parser or gromacs parser from alchemlyb accordingly
check if the file is dhdl or u_nk -> different processing paths
alchemlyb.gmx.read_u_nk can't handle lists?
Gromacs/vmd/colvars doesn't handle pbc consistently; gromacs wraps every atom (by default?) which can produce artifacts when analyzing with colvars.

EzryStIago self-assigned this

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