Umbrellas is a small framework for setting up umbrella replicas in a molecular dynamics umbrella sampling simulation. It is based on the MDAnalysis package and optionally VMD.

Umbrella supports simple US reaction coordinates "out of the box":

• Distance (any xyz component combination)
• Angle
• Dihedral

All that is required is a config file in the following format:

title = <optional text title for this system>

[reaction]
    type = [Distance, Angle, Dihedral] # Choose one. Not case sensitive
    target = <MDAnalysis selection: target residue>
    
    # For Distance
    reference = <MDAnalysis selection: reference residue> # Distance type only
    components = xyz
    
    # Angle and Dihedral
    atoms = <list of atoms> # Comma separated. Required for Angle and Dihedral types

The system will generate a replicas.db file, which is just a text config file containing the replica information. You provide the structure file and Umbrella will help you do the rest.