CV:PTPATHS2PN

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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 / Path

PTPATHS, PTPATHS2P, PTPATHS2PN, PTPATHZ, PATHS2, PATHZ, WORMPOS, WORMANG

Energy

POT

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Definition

The signed path coordinate of the center of mass of the anchor group along a linear path defined by a reference point and a direction. The reference point and the direction point are represented by the centers of mass of two atom groups.

Let ${\mathit{A}}_{com}$ be the anchor center of mass, ${\mathit{R}}_{com}$ the center of mass of the reference group, and ${\mathit{D}}_{com}$ the center of mass of the direction group. The unit direction vector is:

$\mathit{n}=\frac{{\mathit{D}}_{com}-{\mathit{R}}_{com}}{|{\mathit{D}}_{com}-{\mathit{R}}_{com}|}$

Virtual reference points are generated in the positive and negative directions from the reference point:

${\mathit{P}}_i={\mathit{R}}_{com}+i\alpha \mathit{n},i=-N_{-},\dots ,N_{+}$

where $\alpha$ is the spacing between neighbouring virtual reference points, $N_{+}$ is specified by nrefsp, and $N_{-}$ is specified by nrefsn. The collective variable is defined as:

$\xi =\frac{\sum _{i=-N_{-}}^{N_{+}}i\alpha \exp (-\frac{|{\mathit{A}}_{com}-{\mathit{P}}_i{|}^2}{{\beta }^2})}{\sum _{i=-N_{-}}^{N_{+}}\exp (-\frac{|{\mathit{A}}_{com}-{\mathit{P}}_i{|}^2}{{\beta }^2})}$

where $\beta$ is the smoothing parameter. In contrast to CV:PTPATHS and CV:PTPATHS2P, this CV has the dimension of length and its value is a signed distance-like coordinate along the path.

PBC note: The minimum-image convention is applied to the distance vector between the anchor center of mass and each virtual reference point only if the fenable_pbc option is activated. The convention is not used to calculate the centers of mass. It is therefore required that atoms within each group are either covalently bound or are part of a complex that will not be separated or reimaged during a simulation.

Specification

Section name: PTPATHS2PN

Key	Type	Default	Description
name	string		unique CV name
anchor	mask		atoms specifying the anchor point $\mathit{A}$
refpoint	mask		atoms specifying the reference point $\mathit{R}$, which defines the origin of the signed path coordinate
direction	mask		atoms specifying the point $\mathit{D}$; the vector from refpoint to direction defines the path direction
nrefsp	integer		number of virtual reference points in the positive direction $N_{+}$; it must be greater than or equal to 0
nrefsn	integer		number of virtual reference points in the negative direction $N_{-}$; it must be greater than or equal to 0
alpha	real		spacing $\alpha$ between neighbouring virtual reference points; it has the dimension of length
beta	real	alpha	smoothing parameter $\beta$ with the dimension of length

Keys in bold are mandatory.

Additional constraint: The sum nrefsp + nrefsn must be greater than 2.