Root-mean-square deviation (RMSD) of two XYZ structures.

The root-mean-square deviation (RMSD) is calculated, using Kabsch algorithm (1976) for rotation, between two Cartesian coordinates (.xyz) files.

For more information please read RMSD and Kabsch algoritm.

Usage

The code should be executable, so run it via terminal:

./calculate_rmsd molecule1.xyz molecule2.xyz

If it isn't then run it with Python 2.7

python calculate_rmsd molecule1.xyz molecule2.xyz

Citation

1. Kabsch W., 1976, A solution for the best rotation to relate two sets of vectors, Acta Crystallographica, A32:922-923, doi:10.1107/S0567739476001873

2. GitHub: Calculate RMSD for two XYZ structures, http://github.com/charnley/rmsd

Note: some journals may require GitHub commit id.

Examples

Same structure, but translated in space

./calculate_rmsd examples/ethane.xyz examples/ethane_trans.xyz

Same structure, two forcefield minimizations

./calculate_rmsd examples/ethane.xyz examples/ethane_mini.xyz

Same structure, different bondlengths

./calculate_rmsd examples/ethane.xyz examples/ethane_bond.xyz

You can also output (stdout) molecule1's coordinates centered and rotated to molecule2. Useful to visualize the difference.

./calculate_rmsd --output examples/ethane.xyz examples/ethane_trans.xyz

Help

Type ./calculate_rmsd --help or look in the source file.

Credit and Copyright

Jimmy Charnley Kromann and Lars Bratholm