topology  
 RESIDUE SOD  ! Sodium Ion 
 
 GROUP  
       ATOM  SOD   TYPE=SOD  CHARGE=    1.0000  END  
 !END GROUP
 
 
 END {SOD }
 !-----------------------------------------------------------
 
 RESIDUE CL   ! Chloride Anion 
 
 GROUP  
       ATOM  CL1   TYPE=CLA  CHARGE=   -1.0000  END  
 !END GROUP
 
 
 END {CL  }
end

parameter
 NONBONDED  SOD      .1000   2.7297    .1000   2.7297 ! FROM BENOIT ROUX 
 NONBONDED  CLA      .1500   4.2763    .1500   4.2763 ! chloride 
end

segment                                                {*Generate ions     *}

   name="CL- "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in CNS this name is  *}
                                            {*referred to as SEGId.        *}
   chain
   coor
ATOM      1  CL1 CL      1       1.000   0.000   0.000  0.00  0.00      CL- 
   end
   end                                       {*obtain the sequence.        *}
end
                                             
coor
ATOM      1  CL1 CL      1       1.000   0.000   0.000  0.00  0.00      CL- 
end

segment                                                {*Generate ions     *}

   name="NA+ "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in CNS this name is  *}
                                            {*referred to as SEGId.        *}
   chain
   coor
ATOM      1  SOD SOD     1       0.000   0.000   0.000  1.00  0.00      NA+ 
   end
   end                                       {*obtain the sequence.        *}
end
                                             
coor
ATOM      1  SOD SOD     1       0.000   0.000   0.000  1.00  0.00      NA+ 
end

flag excl * incl vdw end

coor copy end

parameter
    nbonds                 
        atom  nbxmod -3  tolerance 0.5  
        repel 0.75  rcon 4.0  rexp 2  cutnb 4.5   
    end
end

evaluate ($xx = 1.8)

while ($xx < 4.9999) loop ANALYS
	evaluate ($xx = $xx + 0.2)
        do (x = $xx) (segid "CL- ")
        energy end
        show ave (dx) (segid "CL- ")
        eval ($fx = $result)
        display DIST	$xx	$vdw
end loop ANALYS

coor swap end

parameter
    nbonds                 
        atom  nbxmod -3  tolerance 0.5  
        repel 0.75  ratt 2.5 rcon 4.0  rexp 2  cutnb 4.5   
    end
end

evaluate ($xx = 1.8)

while ($xx < 4.9999) loop ANALYS
	evaluate ($xx = $xx + 0.2)
        do (x = $xx) (segid "CL- ")
        energy end
        show ave (dx) (segid "CL- ")
        eval ($fx = $result)
        display DIST	$xx	$vdw
end loop ANALYS

stop