Example

The following example shows how to calculate the covariance matrix for all ca atoms:

structure @pti.psf end

dyamics analysis covariance
  
  asci=true
  input=pti_00_100.crd
  begin=1000 skip=1000 stop=100000

  set1=(name ca)
  set2=(name ca)

  output=pti_ca_covar.matrix

end