CV:PMGTD

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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 principal moments of the mass weighted gyration tensor S calculated for the atom group A.

$\xi = \lambda_a - \lambda_b$

where λ are selected principal moments of the gyration tensor. The mass weighted gyration tensor S is defined as

$S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i}$

The eigenvalues of the tensor are $\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2$:

$\bold S = \begin{bmatrix} \lambda_{x}^{2} & 0 & 0 \\ 0 & \lambda_{y}^{2} & 0 \\ 0 & 0 & \lambda_{z}^{2} \end{bmatrix}$

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

Specification

Section name: PMGTD

Key	Type	Default	Description
name	string		unique CV name
group_a	mask		atoms specifying the group A
axis_a	x,y,z		the principal moment axis a
axis_b	x,y,z		the principal moment axis b

Keys in bold are mandatory.