CV:PTPATHS2P

Navigation: Documentation / Collective Variables / CV:PTPATHS2P

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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 along a linear path generated from two reference points. The two reference points are represented by the centers of mass of two atom groups.

Let ${\mathit{A}}_{com}$ be the anchor center of mass and ${\mathit{R}}_{1,com}$ and ${\mathit{R}}_{2,com}$ be the centers of mass of the two reference groups. A set of virtual reference points is generated as:

${\mathit{P}}_i={\mathit{R}}_{1,com}+(i-i_{off})({\mathit{R}}_{2,com}-{\mathit{R}}_{1,com})$

for $i=1,\dots ,N$, where $N$ is specified by the nrefs key. The collective variable is then:

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

where $\alpha$ is the smoothing parameter and $i_{off}$ is the index offset. With the default value $i_{off}=1$, ${\mathit{P}}_1$ corresponds to the first reference point and ${\mathit{P}}_2$ to the second reference point. Additional virtual points are extrapolated along the same line.

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: PTPATHS2P

Key	Type	Default	Description
name	string		unique CV name
anchor	mask		atoms specifying the anchor point $\mathit{A}$
refpoint	mask		atoms specifying a reference point; this key must be provided exactly twice
nrefs	integer		number of virtual reference points $N$; it must be greater than 2
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.