distance <distance-statement> end

--{Nonbonded distance analysis: analyses the nonbonded distances as
   provided by the nonbonded list routines.}

<distance-statement> :==

  from=<atom-selection>
  --{Select subset of atoms for distance analysis.}
  to=<atom-selection>
  --{Select subset of atoms for distance analysis.}
  cuton=<real>
  --{Lower distance cutoff for distance analysis.}
  cutoff=<real>
  --{Upper distance cutoff for distance analysis.
     Distances less than cutoff and less than the list cutoff (cutnb)
     will be used.}
  resdelta=<integer>
  --{If specified then only selected distances between atoms in the same
     segid and sequence separation less or equal to RESDELTA will be used. If 
     both resdelta and reslow are set to -1, no selections based on sequence
     or SEGIDs will be done.}
  reslow=<integer>
  --{If specified then only selected distances between atoms in the same
     segid and sequence separation larger or equal to RESLOW will be used. If 
     both resdelta and reslow are set to -1, no selections based on sequence
     or SEGIDs will be done.}
  ndistance=<integer>
  --{If specified then NDISTANCE distances will be randomly
     picked from the subset of selected interactions from the interaction list.}
  disposition=den|print|rmsd|matrix
  --{Define destination for analysis results.
     rmsd: stores the minimum nonbonded distance for each atom in 
           from set to all atoms in to set in rmsd array.
     print: writes all selected nonbonded distances to the specified 
            output file.
     den: generates DEN distance assignments and writes them to 
          specified file.
     matrix: stores all selected, nonbonded distances in a matrix and 
             then writes the matrix to the specified output file.}
  output=<filename>
  --{File for distance matrix. Default: output.}