View source for CV:RMSDT

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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:RMSDT]]
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{{CVS}}
===Definition===
The root mean square deviation of the structure fitted to the reference structure. The fit is mass weighted.
<center><math>\xi = \sqrt{ \frac {\sum_{i=1}^{N}{ m_i | \bold R_i^' - \bold R_{ref,i}|^2 }} {\sum_{i=1}^{N}{ m_i}} }</math></center>
where '''R'''<sup>'</sup> is the structure superimposed onto the reference structure '''R'''<sub>ref</sub>.

'''PBC note:''' The minimum-image convention is not used.


===Specification===
Section name: '''RMSDT'''
{|
| style="width: 5em;" | '''Key''' 
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|-
| '''group_a'''
| [[Mask format|mask]]
|
| atoms involved in the projection
|-
| '''target'''
| string
|
| name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_a'''
|}
''Keys in bold are mandatory.''