How make FES

luca bellu... at unisi.it
Sat Dec 1 00:05:13 CET 2007


Hi all,
I am trying to get familiar with cp2k metadynamics calculation.
How   can I plot the free energy profile as function  of collective variable ?
What type of information are writed in standar output file like COLVAR,HILL,FREE_ENERGY_INFO etc... 
Can I use these informations for plot free energy profile?

I compiled fep.sopt (In /cp2k/makefile directory I type: make fep.sopt)
and I have a standard input for MM molecular dynamics.
This is  my input file. 
(There are some imprecisions but it is only an example....)

&FORCE_EVAL     
 METHOD FIST
 &MM  
   &FORCEFIELD     
     PARM_FILE_NAME  ./par_amber2charmm.inp
     PARMTYPE   CHM                      
     EI_SCALE14  0.8333
     VDW_SCALE14 0.5
     &SPLINE
       UNIQUE_SPLINE T
       RCUT_NB  10.0
     &END SPLINE
   &END FORCEFIELD                      
  
   &POISSON       
     &EWALD          
       EWALD_TYPE NONE
       ALPHA 0.44
       GMAX   64   
       O_SPLINE 6         
     &END EWALD 
     PERIODIC XYZ         
   &END POISSON

 &END MM
      
 &SUBSYS
      
    &CELL                                             
      ABC  64.000 64.0 57.000
      UNIT ANGSTROM 
      PERIODIC XYZ
    &END CELL                                         

    &TOPOLOGY                                     
      COORD_FILE_NAME   3HS_H_2.coor
      COORDINATE pdb
      CONN_FILE_NAME    3HS.psf
      CONNECTIVITY      UPSF
    &END TOPOLOGY 
 
    &COLVAR   
      &DISTANCE
       ATOMS  5200 1300 
      &END DISTANCE
    &END COLVAR

    &COLVAR   
      &DISTANCE
       ATOMS  5201 250
      &END DISTANCE
    &END COLVAR

    &COLVAR   
      &DISTANCE
       ATOMS  5201 1305
      &END DISTANCE
    &END COLVAR
   &END SUBSYS  

 &END FORCE_EVAL      

&GLOBAL              
  PRINT_LEVEL LOW
  PROJECT        HS_Bind
  RUN_TYPE MD
  SAVE_MEM F
  TRACE F
&END GLOBAL          
 
&MOTION 

  &MD                 
    ENSEMBLE NVT    
    STEPS  500000    
    TIMESTEP 0.80    
    TEMPERATURE   310.0

    &THERMOSTAT
       TYPE NOSE
       REGION GLOBAL
       &NOSE
       &END NOSE
    &END THERMOSTAT 

  &END MD

  &FREE_ENERGY
     &METADYN
        NT_HILLS 100
        WW 1.0E-3 

        &METAVAR
          COLVAR 1
          &WALL
             TYPE QUADRATIC
             POSITION [angstrom] 4.0
             &QUADRATIC
               DIRECTION WALL_PLUS
               K [kcalmol*angstrom^-2] 5.0
             &END QUADRATIC 
          &END WALL
        &END METAVAR

        &METAVAR
          COLVAR 2
          SCALE 0.5
          &WALL
             TYPE QUADRATIC
             POSITION [angstrom] 3.00
             &QUADRATIC
               DIRECTION WALL_PLUS
               K [kcalmol*angstrom^-2] 5.0
             &END QUADRATIC 
          &END WALL
        &END METAVAR

        &METAVAR
          COLVAR 3
          SCALE 0.5
          &WALL
             TYPE QUADRATIC
             POSITION [angstrom] 4.00
             &QUADRATIC
               DIRECTION WALL_PLUS
               K [kcalmol*angstrom^-2] 5.0 
             &END QUADRATIC 
          &END WALL
        &END METAVAR

       &PRINT
          &PROGRAM_RUN_INFO
             EACH 50
            FILENAME=3HS_info    
          &END PROGRAM_RUN_INFO    

          &COLVAR
            EACH 50
            FILENAME=3HS_colvar 
          &END COLVAR

          &HILLS
            EACH 50
            FILENAME=3HS_hills
          &END HILLS
                
        &END PRINT
  
    &END METADYN

    &FREE_ENERGY_INFO
       EACH 50
       FILENAME =3HS_free
    &END FREE_ENERGY_INFO

  &END FREE_ENERGY
 
  &PRINT                  
    &RESTART OFF          
    &END
    &RESTART_HISTORY OFF  
    &END

    &TRAJECTORY
                 
      EACH 50
      FORMAT DCD         
    &END

    &VELOCITIES OFF       
    &END
  &END PRINT 
&END MOTION    



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