CV:PUCK6P

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Navigation: Documentation / Collective Variables / Ring Puckering / CV:PUCK6P


Distance

Angle

Coordination

Shape

Nucleic Acids

Puckering

Special

Energy

Algebra

Definition

Puckering azimuthal angle of six-membered ring is defined as:

The centre of the ring is defined as:

Using two helper vectors RI and RII, the ring z-axis n can be defined as:

For every ring atom, the displacement from the mean ring plane is defined as:

Then two ring-puckering coordinates can be defined as:

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


Specification

Section name: PUCK6P

Key Type Default Description




name string unique CV name
group_a mask atoms specifying the point A, only one atom can be within the group
group_b mask atoms specifying the point B, only one atom can be within the group
group_c mask atoms specifying the point C, only one atom can be within the group
group_d mask atoms specifying the point D, only one atom can be within the group
group_e mask atoms specifying the point E, only one atom can be within the group
group_f mask atoms specifying the point F, only one atom can be within the group

Keys in bold are mandatory. Ring atoms should be specified in the sequence from A to F.