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Missing unwrap of periodic boundary conditions
I noticed that your usage example does not ensure that molecules in the selection are whole. My VDoS functions for any molecules more complex than a single atom will generate garbage if molecules are broken over PBC boundaries.
Solution:
Include "https://github.com/HeydenLabASU/MDA-unwrap-PBC" and use it to make molecules whole (preferred) or use the MDAnalysis transformations (slow)
Naming
This code only computes the vibrational density of states, which by itself has no direct connection to the solvation free energy. Thus the naming of the repo is misleading.
Authors
Don't forget to add people that contributed code to AUTHORS.md
The text was updated successfully, but these errors were encountered:
Missing unwrap of periodic boundary conditions
I noticed that your usage example does not ensure that molecules in the selection are whole. My VDoS functions for any molecules more complex than a single atom will generate garbage if molecules are broken over PBC boundaries.
Solution:
Include "https://github.com/HeydenLabASU/MDA-unwrap-PBC" and use it to make molecules whole (preferred) or use the MDAnalysis transformations (slow)
Naming
This code only computes the vibrational density of states, which by itself has no direct connection to the solvation free energy. Thus the naming of the repo is misleading.
Authors
Don't forget to add people that contributed code to AUTHORS.md
The text was updated successfully, but these errors were encountered: