Section 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.

• Section path: CP2K_INPUT / FORCE_EVAL / SUBSYS / COLVAR / REACTION_PATH / COLVAR / RMSD

• This section cannot be repeated.

• Subsections

  • FRAME

• Keywords

  • ALIGN_FRAMES
  • ATOMS
  • SUBSET_TYPE
  • WEIGHTS

• Keyword descriptions

  ALIGN_FRAMES
  	ALIGN_FRAMES {Logical}
  	Whether the reference frames should be aligned to minimize the RMSD
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  ATOMS
  	ATOMS {Integer} ...
  	Specify indexes of atoms building the subset.
  	This keyword can be repeated and it expects a list of integers.

  SUBSET_TYPE
  	SUBSET_TYPE {Keyword}
  	Define the subsytem used to compute the RMSD
  	This keyword cannot be repeated and it expects precisely one keyword.
  	Default value: ALL
  	List of valid keywords: ALL Without description, yet. LIST Without description, yet. WEIGHT_LIST Without description, yet.

  WEIGHTS
  	WEIGHTS {Real} ...
  	Specify weights of atoms building the subset.
  	This keyword can be repeated and it expects a list of reals.