CV:CNFF

Navigation: Documentation / Collective Variables / CV:CNFF

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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 sum of coordination numbers of atoms from the group A with respect to atoms of the group B using a Fermi-like function.

$\xi = \sum_{i=1}^{group_A} \sum_{j=1}^{group_B} \frac{1}{ 1 + e^{ \beta (d_{ij} - d_{0}) } }$

PBC note: The minimum-image convention is apllied to all atom pair distances if the fenable_pbc option is activated.

Specification

Section name: CNFF

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the group A
group_b	mask		atoms specifying the group B
steepness	real		factor β
reference	real		reference distance d0

Keys in bold are mandatory.