Bemd #28
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Bemd #28
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…er files and constructed pdb/gro fies using mbuild
…the better ordered atoms. These are giving similar results to what we saw on bridges, but the atom ordering is more consistent between monomers
…ions are giving similar results to when I previously ran these on bridges, but theyre updated to run on Alpine and have the better atom numbering so torsion plots and other analysis can be more automated
…ts to calculate CVs in unbiased simulations used later for BEMD simulations
…to this point. This includes simulations with 3 and 4 biased CVs and bespoke simulations for both of those
… a directory with bespoke parameters, but havent run anything it it
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Reopening this PR for recent changes added to the BEMD workflow:
analysis_parameters.ymlfile to each BEMD simulations for plotting parameters that need to be different for different BEMD simulations