remarks TESTFIRS.INP
remarks test the analytic first derivatives for standard potentials

topology @CNS_TOPPAR:protein.top end
parameter @CNS_TOPPAR:protein.param end

segment
  name=tryp
  chain
     @CNS_TOPPAR:protein.link
     sequence
        TRP
     end
  end
end

coor
ATOM      1  HT1 TRP     1       0.101   0.574  -1.385  1.00  0.00      TRYP
ATOM      2  HT2 TRP     1       1.711   0.436  -1.904  1.00  0.00      TRYP
ATOM      3  N   TRP     1       1.067   0.302  -1.101  1.00  0.00      TRYP
ATOM      4  HT3 TRP     1       1.080  -0.689  -0.791  1.00  0.00      TRYP
ATOM      5  CA  TRP     1       1.472   1.192   0.027  1.00  0.00      TRYP
ATOM      6  CB  TRP     1       2.696   2.026  -0.348  1.00  0.00      TRYP
ATOM      7  CG  TRP     1       3.922   1.169  -0.679  1.00  0.00      TRYP
ATOM      8  CD2 TRP     1       4.295   0.679  -1.890  1.00  0.00      TRYP
ATOM      9  CE2 TRP     1       5.424  -0.010  -1.601  1.00  0.00      TRYP
ATOM     10  CE3 TRP     1       3.769   0.774  -3.155  1.00  0.00      TRYP
ATOM     11  CD1 TRP     1       4.813   0.775   0.290  1.00  0.00      TRYP
ATOM     12  NE1 TRP     1       5.727   0.046  -0.320  1.00  0.00      TRYP
ATOM     13  HE1 TRP     1       6.094  -0.743   0.127  1.00  0.00      TRYP
ATOM     14  CZ2 TRP     1       6.138  -0.677  -2.563  1.00  0.00      TRYP
ATOM     15  CZ3 TRP     1       4.472   0.108  -4.148  1.00  0.00      TRYP
ATOM     16  CH2 TRP     1       5.636  -0.605  -3.856  1.00  0.00      TRYP
ATOM     17  C   TRP     1       0.280   2.113   0.309  1.00  0.00      TRYP
ATOM     18  OT1 TRP     1      -0.402   2.481  -0.636  1.00  0.00      TRYP
ATOM     19  OT2 TRP     1      -0.106   2.192   1.459  1.00  0.00      TRYP
END

coor copy end
 
{* c-dielectric, shifting *} 
{* ====================== *}
parameter 
  nbonds
     atom cdie shift eps=1.0
     cutnb=30.0 ctonnb=6.0 ctofnb=8.0
     nbxmod=5 vswitch 
  end
end


test first selection= ( all ) step=0.000001 tol=0.0 end


{* r-dielectric, switching *}
{* ======================= *}
parameter 
  nbonds
     atom rdie switch eps=1.0
     cutnb=30.0 ctonnb=6.0 ctofnb=8.0
     nbxmod=5 vswitch 
  end
end


test first selection= ( all ) step=0.000001 tol=0.0 end

{* repel option  *}
{* ============  *}
flags exclude * include vdw end

parameter 
  nbonds
     atom repel=0.9 rexponent=2 irexponent=2  rconst=110.
 end
end


test first selection= ( all ) step=0.000001 tol=0.0 end

parameter 
  nbonds
     atom repel=0.9 rexponent=4 irexponent=1  rconst=110.
 end
end


test first selection= ( all ) step=0.000001 tol=0.0 end

parameter 
  nbonds
     atom repel=0.9 rexponent=2 irexponent=2  rconst=110.
 end
end


test first selection= ( all ) step=0.000001 tol=0.0 end

parameter 
  nbonds
     atom repel=0.9 rexponent=2 irexponent=1  rconst=110.
 end
end


test first selection= ( all ) step=0.000001 tol=0.0 end

igroup interaction ( chemical O* ) ( chemical N* ) end

do (x=4.) ( chemical O* ) 
do (y=4.) ( chemical O* ) 
do (z=4.) ( chemical O* ) 

do (x=5.) ( chemical N* ) 
do (y=4.) ( chemical N* ) 
do (z=4.) ( chemical N* ) 

parameter 
  nbonds

     atom repel=0.89 rexponent=2 irexponent=1  rconst=110. cutnb=20.
 end
end


parameter
  NONBONDED ( chemical O* ) 0.6469   2.8509       0.6469  2.8509 
  nonbonded ( chemical N* )  0.2384    2.8509      0.2384  2.8509
end
energy end

parameter
  nbfix ( chemical O* ) ( chemical N* ) 1000000. 10.  1000000. 10. 
end
energy end

do ( chemical=N) ( chemical N* )
do (chemical=O) ( chemical O* )

delete selection=( not (chemical O or chemical N ) ) end
igroup interaction ( chemical O* ) ( chemical N* ) end

parameter
   reset
  NONBONDED O  0.6469   2.8509       0.6469  2.8509 
  nonbonded N  0.2384    2.8509      0.2384  2.8509
end

energy end

parameter
  nbfix O N  1000000. 10.  1000000. 10.
end

energy end


stop