CV:RMSDT

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Definition

The root mean square deviation of the structure fitted to the reference structure. The fit is mass weighted.

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi = \sqrt{ \frac {\sum_{i=1}^{N}{ m_i | \bold R_i^' - \bold R_{ref,i}|^2 }} {\sum_{i=1}^{N}{ m_i}} }}

where R^' is the structure superimposed onto the reference structure R_ref.

PBC note: The minimum-image convention is not used.

Specification

Section name: RMSDT

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms involved in the projection
target	string		name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a

Keys in bold are mandatory.