jax_md_mod.custom_quantity.init_rmsd

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jax_md_mod.custom_quantity.init_rmsd#

init_rmsd(reference_positions, displacement_fn, reference_box, idx=None, weights=None)[source]#

Initializes the root mean squared distance from a reference structure.

The RMSD is a common measure in the analysis of macrostructures [1]. The weighted RMSD between a current positions $p$ and reference positions $q$ is defined as

\[\mathrm{RMSD} = \sqrt{\frac{\sum_{i=1}^n w_i || (Rp + t )- q||^2}{\sum_{i=1}^n w_i}},\]

where $R$ and $t$ define a rigid body motion that minimizes the RMSD [2].

Parameters:

  • reference_positions – Reference positions including all atoms.

  • displacement_fn – Function to compute displacement between particles.

  • reference_box – Reference box of the reference structure.

  • idx – Indices selecting only the structure of interest, e.g. for a protein in a solvent.

  • weights – Weight the rmsd, e.g., with masses of the particles.

References

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