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

Type: logical
Default: F
Lone keyword: T
Usage: ALIGN_FRAMES

Description: Whether the reference frames should be aligned to minimize the RMSD

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ATOMS

Type: integer[ ]
Repeatable: yes
Usage: ATOMS {integer} {integer} ..

Description: Specify indexes of atoms building the subset.

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SUBSET_TYPE

Type: enum
Default: ALL
Usage: SUBSET_TYPE ALL

Description: 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.

Valid values:

• ALL

• LIST

• WEIGHT_LIST

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WEIGHTS

Type: real[ ]
Repeatable: yes
Usage: weightS {real} {real} ..

Description: Specify weights of atoms building the subset. It is used only with WEIGHT_LIST

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