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_FRAME

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 [Edit on GitHub]

WEIGHTS: real

Keyword can be repeated.

Usage: weightS {real} {real} ..

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