View source for CV:MDIS

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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:MDIS]]
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{{CVS}}
===Definition===
The minimum value of atom pair distances. To ensure that the collective variable is a continuous function a probabilistic definition is used. This is an approximation providing good estimate of minimal distance. In most cases it provides a value slighter higher than a real minimum distance. However for degenerate situations, where more than one atom pair distance is very close to a minimum value, the value of collective variable will be lower than this minimum value.  

<center><math>\xi = - \beta * ln \left(  \sum_{i=1}^{pairs} e^{ - \frac{d_i}{\beta} }\right) </math></center>

Non-degenerate case:
<center><math>\xi \geq d_{minimum}</math></center>

Degenerate case (n<sub>g</sub> is degree of degeneracy):
<center><math>\xi \doteq d_{minimum} - \beta*ln(n_g)</math></center>

'''PBC note:''' The minimum-image convention is apllied to all atom pair distances if the [[General setup|fenable_pbc]] option is activated.


===Specification===
Section name: '''MDIS'''
{|
| style="width: 5em;" | '''Key''' 
| style="width: 10em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|-
| beta
| real
| 1.0
| factor &beta;
|-
| '''pair'''
| [[Mask format|mask]] [[Mask format|mask]]
|
| two masks specifying the atom pair. Each mask can hold only one atom. This line is repeating until all atom pairs are specified.
|}
''Keys in bold are mandatory.''