CV:PTPATHS

Navigation: Documentation / Collective Variables / CV:PTPATHS

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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 path coordinate of the center of mass of the anchor group relative to a set of explicitly defined reference points. Each reference point is represented by the center of mass of one atom group.

For the anchor center of mass ${\mathit{A}}_{com}$ and the centers of mass of the reference points ${\mathit{R}}_{i,com}$, the collective variable is defined as:

$\xi =\frac{\sum _{i=1}^N(i-i_{off})\exp (-\frac{|{\mathit{A}}_{com}-{\mathit{R}}_{i,com}{|}^2}{{\alpha }^2})}{(N-1)\sum _{i=1}^N\exp (-\frac{|{\mathit{A}}_{com}-{\mathit{R}}_{i,com}{|}^2}{{\alpha }^2})}$

where $N$ is the number of reference points, $\alpha$ is the smoothing parameter, and $i_{off}$ is the index offset. With the default value $i_{off}=1$, the CV is approximately normalized to the interval from 0 to 1.

PBC note: The minimum-image convention is applied to the distance vector between the anchor center of mass and each reference-point center of mass 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: PTPATHS

Key	Type	Default	Description
name	string		unique CV name
anchor	mask		atoms specifying the anchor point $\mathit{A}$
refpoint	mask		atoms specifying one reference point ${\mathit{R}}_i$; this key is repeated for all reference points
alpha	real		smoothing parameter $\alpha$ with the dimension of length
ioffset	integer	1	index offset $i_{off}$ used to define the path coordinate origin

Keys in bold are mandatory.