CV:CNGRF

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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 coordination numbers of the point A with respect to atoms of the group B using a rational function.

$\xi = \sum_{i=1}^{group_B} \frac{ 1 - \left( \frac{d_{iA} - d_{offset}}{d_{o}} \right) ^ n }{ 1 - \left( \frac{d_{iA}- d_{offset}}{d_{o}} \right) ^ m }$ $d_{iA} = | \bold x_i - \bold A_{com} |$

PBC note: The minimum-image convention is apllied to distances d_iA if the fenable_pbc option is activated. The convention is not used to calculate the center of mass of the pont A. It is therefore required that atoms within a group are either covalently bound or are part of complex that will not be separated or reimaged during a simulation.

Specification

Section name: CNGRF

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the point A
group_b	mask		atoms specifying the group B
offset	real		the value of doffset
reference	real		the reference distance d0
npower	integer		the value of n-power
mpower	integer		the value of m-power

Keys in bold are mandatory.