molecular dynamics run
 &cntrl
     nmropt=1, vlimit=20
    imin=0,irest=0,ntx=1,
    tempi=0.0,temp0=300,tautp=0.5
    ntt=1,npscal=1,nsnb=25
    ntp=0,ntb=1,ntr=1
    ntc=2,ntf=2,scee=1.2,
    nstlim=25000,dt=0.002,
    ntwx=500,ntpr=25,ntwr=500,
    cut=12.0,
    lastist = 3500000,lastrst = 5000000
 &end
 &wt
   type='TEMP0',istep1=0,istep2=2500,
                value1=0.0,value2=50.0,
 &end
 &wt
   type='TEMP0',istep1=2500,istep2=5000,
                value1=50.0,value2=100.0,
 &end
&wt
   type='TEMP0',istep1=5000,istep2=7500,
                value1=100.0,value2=150.0,
 &end
 &wt
   type='TEMP0',istep1=7500,istep2=10000,
                value1=150.0,value2=200.0,
 &end
 &wt
   type='TEMP0',istep1=10000,istep2=15000,
                value1=200.0,value2=300.0,
 &end
 &wt
   type='TEMP0',istep1=15000,istep2=25000,
                value1=300.0,value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
Restrain the Protein heavy atoms I
50.0
FIND
 *  C   *  *
 *  CA  *  *
 *  CB  *  *
 *  CC  *  *
 *  CD  *  *
 *  CK  *  *
 *  CM  *  *
 *  CN  *  *
 *  CQ  *  *
SEARCH
RES 1  342
END
Restrain the Protein heavy atoms II
50.0
FIND
 *  CR  *  *
 *  CT  *  *
 *  CV  *  *
 *  CW  *  *
 *  C*  *  *
 *  CY  *  *
 *  CZ  *  *
 *  N   *  *
 *  NA  *  *
SEARCH
RES 1  342
END
Restrain the Protein heavy atoms III
50.0                              
FIND                               
 *  NC  *  *                       
 *  N2  *  *                       
 *  N3  *  *                       
 *  NT  *  *                       
 *  N*  *  *                       
 *  NY  *  *
 *  NB  *  *                       
 *  O   *  *                       
 *  O2  *  *                       
SEARCH                             
RES 1  342                         
END
Restrain the Protein heavy atoms III 
50.0                                
FIND
 *  OH  *  *                       
 *  OS  *  *                                 
 *  P   *  *          
 *  S   *  *           
 *  SH  *  *                              
SEARCH                               
RES 1  342                           
END
Restrain the lig heavy atoms I
50.0
FIND
 *  ca  *  *
 *  c   *  *
 *  ce  *  *  
 *  c3  *  *
 *  n2  *  *
 *  o   *  *
 *  os  *  *
 *  oh  *  *
SEARCH
RES 343
END
END
