CV:PUCK5P

Navigation: Documentation / Collective Variables / Ring Puckering / CV:PUCK5P

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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

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

$\xi =q_{\varphi }=atan2\left(\frac{q_y}{q_x}\right)$

The centre of the ring is defined as:

${\mathbf{𝐑}}_{cog}=\sum _{i=1}^5{\mathbf{𝐗}}_i$

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

${\mathbf{𝐑}}_I=\sum _{i=1}^5({\mathbf{𝐗}}_i-{\mathbf{𝐑}}_{cog})sin\left(\frac{2\pi [i-1]}{5}\right)$ ${\mathbf{𝐑}}_{II}=\sum _{i=1}^5({\mathbf{𝐗}}_i-{\mathbf{𝐑}}_{cog})cos\left(\frac{2\pi [i-1]}{5}\right)$ $\mathbf{𝐧}=\frac{{\mathbf{𝐑}}_I\times {\mathbf{𝐑}}_{II}}{|{\mathbf{𝐑}}_I\times {\mathbf{𝐑}}_{II}|}$

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

$z_i=\mathbf{𝐧}\cdot ({\mathbf{𝐗}}_i-{\mathbf{𝐑}}_{cog})$

Then two ring-puckering coordinates can be defined as:

$q_x=\sqrt{\frac{2}{5}}\sum _{i=1}^5{z}_{i}cos\left(\frac{4\pi [i-1]}{5}\right)$ $q_y=-\sqrt{\frac{2}{5}}\sum _{i=1}^5{z}_{i}sin\left(\frac{4\pi [i-1]}{5}\right)$

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

Specification

Section name: PUCK5P

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

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