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Histidine is denoted as HIS in the .top-file, when the .top-file is generated from a amino acid sequence via pymol fab and pdb2gmx. However, the amber force field encompasses not HIS but HIP, HID, and…
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At the moment we automatically remove plumed variables from the plumed file if a bond is broken. This is the behavior we want if we only do homolysis but for homolysis/recombination simulations or som…
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https://github.com/hits-mbm-dev/kimmdy/blob/8e9c383b4075ddf9c271d047ee7dcd8ae46395d3/www/colbuilder_files/change_crosslink_atom_names.py#L3
@ehhartmann I missed this in the review. Where is `functi…
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At least two areas in the code still need information from aberff99sb:
1. The Topology module uses `aminoacids.rtp` to use the residuetypes (e.g. for a partial charge lookup after a binding event)
2…
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https://github.com/graeter-group/grappa/blob/fc1680f10a8889c9f1acb305b4c4d35b03f062ab/src/grappa/data/molecule.py#L78
how should this work if the default is none?
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So.... I have the urge for a "small" refactor that nonetheless touches most parts of kimmdys code and need your (@KRiedmiller @ehhartmann ) input if this is a good idea.
Our RecipeSteps use atom `i…
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Gromacs simulation continuation relies on the cpt file which (I think) we can't modify to restart after a reaction. This is why we supply coordinates, velocities and other variables with the trr, edr …
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From a user perspective it is confusing that the kmc type is changed by a reaction plugin. I think it should be a setting in the kimmdy config.yml, not of the individual plugins.
(written by Eric)
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https://userguide.mdanalysis.org/stable/formats/reference/tpr.html#supported-versions
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For homolysis with a very big system, aggregate_reactions in the recipe_collection freezes KIMMDY for unknown duration.
Workaround is to remove the aggregate_reactions call in runmanager._decide_re…