CV:DD

Navigation: Documentation / Collective Variables / CV:DD

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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 difference between two distances. Each distance is calculated as a distance between the center of mass of two groups of atoms.

$\xi = | \bold A_{com} - \bold B_{com} | - | \bold C_{com} - \bold D_{com} |$

PBC note: The minimum-image convention is apllied to the distances |AB| and |CD| only if the fenable_pbc option is activated. The convention is not used to calculate the center of mass. 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. The convention is not also applied to the distance difference result.

Specification

Section name: DD

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the point A
group_b	mask		atoms specifying the point B
group_c	mask		atoms specifying the point C
group_d	mask		atoms specifying the point D

Keys in bold are mandatory.