remarks param6.inp
remarks more tests for learning and reducing parameters
remarks  Axel T. Brunger
remarks ==================================

topology reset @CNS_TOPPAR:protein-allhdg5-4.top end   {* this is the DG-version of this file *}

segment
   name="TRYP"
   chain
      @CNS_TOPPAR:protein-allhdg5-4.link
      sequence trp  end
  end
end

parameter 
        @CNS_TOPPAR:protein-allhdg5-4.param 
        nbonds repel = 0.8 end
end

coor
ATOM      1  CA  TRP     1       1.331   1.246   0.096  1.00  0.00      TRYP
ATOM      2  HA  TRP     1       1.571   0.780   1.039  1.00  0.00      TRYP
ATOM      3  CB  TRP     1       2.535   2.085  -0.418  1.00  0.00      TRYP
ATOM      4  HB1 TRP     1       2.239   2.586  -1.319  1.00  0.00      TRYP
ATOM      5  HB2 TRP     1       2.751   2.850   0.315  1.00  0.00      TRYP
ATOM      6  CG  TRP     1       3.804   1.229  -0.669  1.00  0.00      TRYP
ATOM      7  CD1 TRP     1       4.717   0.866   0.299  1.00  0.00      TRYP
ATOM      8  HD1 TRP     1       4.659   1.099   1.355  1.00  0.00      TRYP
ATOM      9  CD2 TRP     1       4.351   0.653  -1.938  1.00  0.00      TRYP
ATOM     10  NE1 TRP     1       5.724   0.123  -0.275  1.00  0.00      TRYP
ATOM     11  HE1 TRP     1       6.486  -0.256   0.211  1.00  0.00      TRYP
ATOM     12  CE2 TRP     1       5.557  -0.035  -1.629  1.00  0.00      TRYP
ATOM     13  CE3 TRP     1       3.937   0.642  -3.303  1.00  0.00      TRYP
ATOM     14  HE3 TRP     1       3.030   1.139  -3.603  1.00  0.00      TRYP
ATOM     15  CZ2 TRP     1       6.307  -0.689  -2.607  1.00  0.00      TRYP
ATOM     16  HZ2 TRP     1       7.219  -1.201  -2.337  1.00  0.00      TRYP
ATOM     17  CZ3 TRP     1       4.699  -0.019  -4.279  1.00  0.00      TRYP
ATOM     18  HZ3 TRP     1       4.371  -0.014  -5.308  1.00  0.00      TRYP
ATOM     19  CH2 TRP     1       5.879  -0.680  -3.932  1.00  0.00      TRYP
ATOM     20  HH2 TRP     1       6.459  -1.186  -4.691  1.00  0.00      TRYP
ATOM     21  C   TRP     1       0.137   2.181   0.303  1.00  0.00      TRYP
ATOM     22  O   TRP     1      -0.629   2.346  -0.631  1.00  0.00      TRYP
ATOM     23  OXT TRP     1       0.010   2.715   1.393  1.00  0.00      TRYP
ATOM     24  N   TRP     1       0.945   0.198  -0.894  1.00  0.00      TRYP
ATOM     25  HT1 TRP     1       1.555  -0.635  -0.775  1.00  0.00      TRYP
ATOM     26  HT2 TRP     1      -0.048  -0.074  -0.740  1.00  0.00      TRYP
ATOM     27  HT3 TRP     1       1.057   0.571  -1.858  1.00  0.00      TRYP
END

parameter
   bond ( all ) ( all ) 400. TOKEN
   angle ( all ) ( all ) ( all ) 400. TOKEN
   improper ( all ) ( all ) (all) ( all ) 
           400. TOKEN TOKEN
   nonbonded ( all ) 0.1 2. 0.1 2. 
end

parameter
   ?
   learn initialize selection=( all ) mode=nostat end
   learn accumulate end
   learn terminate end
   reduce mode=average end
   ?
end

energy end



do ( segid="A" ) ( all ) 

duplicate selection=( all ) segid="B" end

coor translate vector=( 100. 0. 0. ) selection=( segid "B" ) end

ident ( store1 ) ( all )
do ( chemical=encode ( store1 ) ) ( segid "B" ) 

parameter
   learn initialize selection=( segid "B" ) end
   learn accumulate end
   learn terminate end
   bond ( segid "B" ) ( segid "B" ) 400. TOKEN
   angle ( segid "B" ) ( segid "B" ) (segid "B") 400. TOKEN
   improper ( segid "B" ) ( segid "B" ) (segid "B") ( segid "B" ) 
           400. TOKEN TOKEN
   nonbonded ( segid "B" )  0.1 2. 0.1 2.  

   verbose
end

do (x=x+0.3 ) ( name c* ) 

energy end

igroup interactio=( segid "A" ) ( segid "A" ) end
energy end

igroup interactio=( segid "B" ) ( segid "B" ) end
energy end


stop