CV:OPOS2

Navigation: Documentation / Collective Variables / CV:OPOS2

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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 absolute position of the point along a selected axis of the superimposed coordinate system of a reference structure. Any axis of the superimposed coordinate system can be selected.

$\xi =A_{com,z}^{\text{'}}$

The relation between re-oriented (') and native coordinate system is given by the transformation matrix T:

${\mathbf{𝐀}}_{com}^{\text{'}}=\mathbf{𝐓}{\mathbf{𝐀}}_{com}$

Specification

Section name: OPOS2

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the point A
reference_a	string		name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a
group_b	mask		atoms specifying the point B
direction	x, y, z		select axis in the superimposed coordinate system

Keys in bold are mandatory.