[CP2K-user] umbrella integration

Wei Zhang zwei88... at gmail.com
Sat Dec 22 15:19:32 UTC 2018
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Dear all,
I am studying cp2k, and I want to use umbrella integration to calculate the 
PMF of NaCl. Here follows the example of the input files of NaCl solution, 
and the distance of Na-Cl is 2.5 A. Some part of the output file was 
followed. I am wondering what meaning of (eval_cov_matrix          82      
    84   4.8791450923533191        1.2895562591097587E-004) and how could 
them be used to calculate the free energy?

Many thanks for your help.
Merry Chrismas!

Wei

#
# NaCl in water
#
&FORCE_EVAL
  METHOD FIST
  &MM
    &FORCEFIELD
      &SPLINE
        EMAX_SPLINE 300000.0
      &END
      &BEND
        ATOMS H O H
        KIND HARMONIC
        K [rad^-2kcalmol] 110.0
        THETA0 [deg] 104.52
      &END BEND
      &BOND
        ATOMS O H
        KIND HARMONIC
        K [angstrom^-2kcalmol] 900.0 
        R0 [angstrom] 0.9572
      &END BOND
      &CHARGE
        ATOM Na
        CHARGE 1.0
      &END CHARGE
      &CHARGE
        ATOM Cl
        CHARGE -1.0
      &END CHARGE
      &CHARGE
        ATOM O
        CHARGE -0.834
      &END CHARGE
      &CHARGE
        ATOM H
        CHARGE 0.417
      &END CHARGE
      &NONBONDED
        &LENNARD-JONES
          atoms O O
          EPSILON [kcalmol]  0.152073
          SIGMA   [angstrom] 3.1507
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms O H
          EPSILON [kcalmol] 0.0836
          SIGMA [angstrom] 1.775
          RCUT  [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms H H
          EPSILON [kcalmol]  0.04598
          SIGMA   [angstrom] 0.400
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Na Na
          EPSILON [kcalmol]  0.0469
          SIGMA   [angstrom] 2.7275
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Na O
          EPSILON [kcalmol]  .08445
          SIGMA   [angstrom] 2.93
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Na H
          EPSILON [kcalmol]  .0464
          SIGMA   [angstrom] 1.5637
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Na Cl
          EPSILON [kcalmol]  .0838
          SIGMA   [angstrom] 3.63
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Cl Cl
          EPSILON [kcalmol]  0.150
          SIGMA   [angstrom] 4.54
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Cl O
          EPSILON [kcalmol]  .151
          SIGMA   [angstrom] 3.84
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
        &LENNARD-JONES
          atoms Cl H
          EPSILON [kcalmol]  .083
          SIGMA   [angstrom] 2.47
          RCUT    [angstrom] 11.4
        &END LENNARD-JONES
      &END NONBONDED
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE spme
        ALPHA .3
        GMAX 12
        O_SPLINE 6
      &END EWALD
    &END POISSON
  &END MM
  &SUBSYS
    &CELL
      ABC 12.4138 12.4138 12.4138
    &END CELL
     &COORD
@INCLUDE 'coord-2.5'
     &END COORD
     &COLVAR
      &DISTANCE
        ATOMS 190 191
      &END DISTANCE
      !&PRINT
         !&PROGRAM_RUN_INFO ON
          ! &EACH
           !   MD  1
    !       &END EACH
        !&END PROGRAM_RUN_INFO
      !&END PRINT
     &END COLVAR
    &TOPOLOGY
      CONNECTIVITY GENERATE
      &GENERATE
        BONDLENGTH_MAX 7
      &END
    &END
  &END SUBSYS
&END FORCE_EVAL

&MOTION
 &CONSTRAINT
    &COLLECTIVE
      COLVAR 1
      INTERMOLECULAR
      TARGET [angstrom] 2.5
      &RESTRAINT
        K [kcalmol] 200
      &END RESTRAINT
    &END COLLECTIVE
    !&LAGRANGE_MULTIPLIERS
      !COMMON_ITERATION_LEVELS 3
    !&END
 &END CONSTRAINT
 &MD
   ENSEMBLE NVT
   TIMESTEP 0.5
   STEPS    2000
   TEMPERATURE 350
   &THERMOSTAT
     REGION    GLOBAL              
     &NOSE
       LENGTH 3
       YOSHIDA 3
       TIMECON 1000
       MTS 2
     &END NOSE
   &END
   &PRINT 
     &ENERGY
        &EACH
           MD 1
        &END
     &END ENERGY
     !&PROGRAM_RUN_INFO
       ! &EACH
        !   MD 1
        !&END
     !&END PROGRAM_RUN_INFO
   &END PRINT
 &END MD
 &PRINT 
  &TRAJECTORY
     &EACH
        MD 1
     &END
  &END
  &VELOCITIES OFF
  &END VELOCITIES
  &FORCES OFF
  &END FORCES
  &RESTART_HISTORY OFF
  &END RESTART_HISTORY 
  &RESTART OFF
  &END RESTART
 &END PRINT
 &GEO_OPT
   OPTIMIZER LBFGS
 &END

&FREE_ENERGY
    METHOD UI
    &UMBRELLA_INTEGRATION
     &CONVERGENCE_CONTROL
        EPS_CONV 0.5
        COARSE_GRAINED_WIDTH     3
        MAX_COARSE_GRAINED_WIDTH 3
        COARSE_GRAINED_POINTS    2
     &END CONVERGENCE_CONTROL
     &UVAR
       COLVAR 1
     &END UVAR
    &END UMBRELLA_INTEGRATION
    
    &FREE_ENERGY_INFO
      COMMON_ITERATION_LEVELS 1
      &EACH 
        MD 1
      &END EACH
    &END FREE_ENERGY_INFO
  &END
&END MOTION
&GLOBAL
  PROJECT NACL-CONSTRAINED-2.5-3
  RUN_TYPE MD
  IOLEVEL LOW
  &PRINT
   PHYSCON
  &END PRINT
&END GLOBAL

*output:*

 ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):            
 -1.140112705278208

 COLVAR::   4.8903632470564613     
          82          82

 *******************************************************************************
 ENSEMBLE TYPE                =                                            
  NVT
 STEP NUMBER                  =                                            
   82
 TIME [fs]                    =                                        
41.000000
 CONSERVED QUANTITY [hartree] =                              
-0.846052947201E+00

                                              INSTANTANEOUS            
 AVERAGES
 CPU TIME [s]                 =                        0.01                
 0.01
 ENERGY DRIFT PER ATOM [K]    =          0.373834318693E+00  
 0.118177365928E-01
 POTENTIAL ENERGY[hartree]    =         -0.114011270528E+01  
-0.113335123442E+01
 KINETIC ENERGY [hartree]     =          0.292558333950E+00  
 0.286028884488E+00
 TEMPERATURE [K]              =                     324.149              
316.915
 *******************************************************************************


 ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):            
 -1.145923868073005

 COLVAR::   4.8794156731299481     
          83          83

 *******************************************************************************
 ENSEMBLE TYPE                =                                            
  NVT
 STEP NUMBER                  =                                            
   83
 TIME [fs]                    =                                        
41.500000
 CONSERVED QUANTITY [hartree] =                              
-0.846293102603E+00

                                              INSTANTANEOUS            
 AVERAGES
 CPU TIME [s]                 =                        0.01                
 0.01
 ENERGY DRIFT PER ATOM [K]    =         -0.232075005042E-01  
 0.113957457844E-01
 POTENTIAL ENERGY[hartree]    =         -0.114592386807E+01  
-0.113350271193E+01
 KINETIC ENERGY [hartree]     =          0.298118106873E+00  
 0.286174537770E+00
 TEMPERATURE [K]              =                     330.309              
317.076
 *******************************************************************************


 ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):            
 -1.151438173429435

 COLVAR::   4.8676563568735487     
          84          84
 *******************************************************************************
                             FREE ENERGY CALCULATION

          84           3
          82          84
 eval_cov_matrix          82          84   4.8791450923533191        
1.2895562591097587E-004
          79          81
 eval_cov_matrix          79          81   4.9088196261817298        
6.8493458343255043E-005
          76          78
 eval_cov_matrix          76          78   4.9276165349320822        
1.7493356395448245E-005
          73          75
 eval_cov_matrix          73          75   4.9331984582015895        
4.2806313160781428E-007
          70          72
 eval_cov_matrix          70          72   4.9248292229843216        
2.5841844411900183E-005
          67          69
 eval_cov_matrix          67          69   4.9034737225850238        
8.2163081351893652E-005
          64          66
 eval_cov_matrix          64          66   4.8717144712694900        
1.4267166679360344E-004
          61          63
 eval_cov_matrix          61          63   4.8334807396779205        
1.7780849109527708E-004
          58          60
 eval_cov_matrix          58          60   4.7936121609791531        
1.6946047939825348E-004
          55          57
 eval_cov_matrix          55          57   4.7572917091301408        
1.2068974226764340E-004


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