View source for PTPATHS

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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PTPATHS]]
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{{CVS}}
===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 <math>\boldsymbol A_{com}</math> and the centers of mass of the reference points <math>\boldsymbol R_{i,com}</math>, the collective variable is defined as:

<center><math>
\xi =
\frac{
\sum_{i=1}^{N} (i-i_{off}) \exp\left(-\frac{|\boldsymbol A_{com}-\boldsymbol R_{i,com}|^2}{\alpha^2}\right)
}{
(N-1)\sum_{i=1}^{N} \exp\left(-\frac{|\boldsymbol A_{com}-\boldsymbol R_{i,com}|^2}{\alpha^2}\right)
}
</math></center>

where <math>N</math> is the number of reference points, <math>\alpha</math> is the smoothing parameter, and <math>i_{off}</math> is the index offset. With the default value <math>i_{off}=1</math>, 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 [[General setup|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'''
{|
| style="width: 7em;" | '''Key''' 
| style="width: 7em;" | '''Type'''
| style="width: 7em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|-
| '''anchor'''
| [[Mask format|mask]]
|
| atoms specifying the anchor point <math>\boldsymbol A</math>
|-
| '''refpoint'''
| [[Mask format|mask]]
|
| atoms specifying one reference point <math>\boldsymbol R_i</math>; this key is repeated for all reference points
|-
| '''alpha'''
| real
|
| smoothing parameter <math>\alpha</math> with the dimension of length
|-
| '''ioffset'''
| integer
| 1
| index offset <math>i_{off}</math> used to define the path coordinate origin
|}
''Keys in bold are mandatory.''