# RMSD

Section to define a CV as function of RMSD computed with respect to given reference configurations. For 2 configurations the colvar is equal to: ss = (RMSDA-RMSDB)/(RMSDA+RMSDB), while if only 1 configuration is given, then the colvar is just the RMSD from that frame. [Edit on GitHub]

Subsections

- FRAME

## Keywords

- ALIGN_FRAMES

- ATOMS

- SUBSET_TYPE

- WEIGHTS

## Keyword descriptions

ALIGN_FRAMES: logical = F

  Lone keyword: `T`

  Usage: ALIGN_FRAMES

  Whether the reference frames should be aligned to minimize the RMSD [Edit on GitHub]

ATOMS: integer[ ]

  Keyword can be repeated.

  Usage: ATOMS {integer} {integer} ..

  Specify indexes of atoms building the subset. [Edit on GitHub]

SUBSET_TYPE: enum = ALL

  Usage: SUBSET_TYPE ALL

  Valid values:

  - `ALL`

  - `LIST`

  - `WEIGHT_LIST`

  Define the subsytem used to compute the RMSD. With ALL the displacements are mass-weighted, with LIST all weights are set to 1, with WEIGHT_LIST a list of weights is expected from input. [Edit on GitHub]

WEIGHTS: real[ ]

  Keyword can be repeated.

  Usage: weightS {real} {real} ..

  Specify weights of atoms building the subset. It is used only with WEIGHT_LIST [Edit on GitHub]