Metadynamics, Reflective wall, Colvar, Torsion

Ghazaleh Zm gazel... at gmail.com
Tue Nov 22 23:19:08 CET 2016


Dear All 

I am a beginner in CP2K and I need some help for continuing my project. 
I have a small molecule which rotates and translates during the trajectory 
after running CP2K MD. I need to caculate the IR spectra so the rotation 
and translation of the molecules is unpleasant and I only need the 
vibrations. 
I have been recommended to use the Reflective Wall in Metadynamics so that 
the atoms do not rotate freely. 
I did not find much helpful material online to learn about these stuff 
(FREE ENERGY section, especially WALL REFLECTIVE, as well as the section 
COLVAR, TORSION). Can someone give me links to detailed explanation of how 
to use these sections? 

I should also determine the atom indexes which I do not want to move (in 
the section COLVAR, TORSION)
which atoms should I specify while I would like the whole 2 molecules 
(dimer) not to rotate? 

That would be perfect if there exist some tutorial which contains detailed 
explanation of these parts. 
I copy my input file here, but with these specifications that I made, it 
did not work and the molecules still rotate and translate. 

Thanks 
Ghazaleh

&GLOBAL
PROJECT_NAME thion_dimer-dft-MD
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
#-----------------------------------------------------------------------------------------------------------------------------------------------------------
&FORCE_EVAL
&DFT
BASIS_SET_FILE_NAME  GTH_BASIS_SETS
POTENTIAL_FILE_NAME  GTH_POTENTIALS
        &MGRID
        CUTOFF 500
        REL_CUTOFF 30
        NGRIDS 4
        &END MGRID
        &SCF
        SCF_GUESS ATOMIC
        MAX_SCF   300
                &OT
                MINIMIZER DIIS
                PRECONDITIONER FULL_SINGLE_INVERSE
                &END OT
                &PRINT
                        &RESTART
                                &EACH
                                MD 2000
                                &END EACH
                        &END RESTART
                &END PRINT
        &END SCF
        &LOCALIZE
        METHOD CRAZY
        MAX_ITER 2000
                &PRINT
                        &WANNIER_CENTERS
                        IONS+CENTERS
                        FILENAME =thion_dimer-dft-MD-wc.xyz
                                &EACH
                                MD 5
                                &END EACH
                        &END WANNIER_CENTERS
                &END PRINT
        &END LOCALIZE
        &XC
                &XC_FUNCTIONAL  BLYP
                &END XC_FUNCTIONAL
                &XC_GRID
                XC_DERIV NN10_SMOOTH
                XC_SMOOTH_RHO NN10
                &END XC_GRID
                &VDW_POTENTIAL
                POTENTIAL_TYPE PAIR_POTENTIAL
                        &PAIR_POTENTIAL
                        TYPE DFTD3
                        PARAMETER_FILE_NAME dftd3.dat
                        REFERENCE_FUNCTIONAL  BLYP
                        &END PAIR_POTENTIAL
                &END VDW_POTENTIAL
        &END XC
&PRINT
      &MOMENTS
       PERIODIC FALSE
       &EACH
         MD 1
       &END
       MAX_MOMENT 1
       FILENAME =dipole-thion_dimer-dft-MD.traj
      &END MOMENTS
     &END
&END DFT
#---------------------------------------------------------------------------------------------------------------------------------------------------------
&SUBSYS
        &CELL
        ABC 28       28       28
        ALPHA_BETA_GAMMA 90.00  90.00  90.00
        PERIODIC XYZ   ! => Periodicity of the system
        &END CELL
        &TOPOLOGY
        COORD_FILE_NAME  min-thion_dimer-lf.xyz
        COORD_FILE_FORMAT         xyz
        &END TOPOLOGY
&KIND O
      BASIS_SET DZVP-GTH
      POTENTIAL GTH-BLYP-q6
    &END KIND
&KIND C
      BASIS_SET DZVP-GTH
      POTENTIAL GTH-BLYP-q4
    &END KIND
&KIND N
      BASIS_SET DZVP-GTH
      POTENTIAL GTH-BLYP-q5
    &END KIND
!&KIND D
!       BASIS_SET DZVP-GTH
!       POTENTIAL GTH-BLYP-q1
!       MASS 2.0
!       ELEMENT H
!    &END KIND
&KIND H
       BASIS_SET DZVP-GTH
       POTENTIAL GTH-BLYP-q1
    &END KIND
&KIND S
       BASIS_SET DZVP-GTH
       POTENTIAL GTH-BLYP-q6
    &END KIND
&COLVAR
       &TORSION
         ATOMS              1             3              8              9
       &END TORSION
     &END COLVAR
&END SUBSYS
&END FORCE_EVAL
#--------------------------------------------------------------------------------------------------------------------------------------------------------
&MOTION
        &MD
        ENSEMBLE NVT
        STEPS   20000
        TIMESTEP 0.5
        TEMPERATURE 300.0
        COMVEL_TOL 1e-8
        ANGVEL_ZERO T
        ANGVEL_TOL 1e-12
                &THERMOSTAT
                TYPE NOSE
                        &NOSE
                        TIMECON 100
                        &END NOSE
                &END THERMOSTAT
        &END MD
&FREE_ENERGY
     METHOD  METADYN
     &METADYN
       MIN_DISP    -1.0000000000000000E+00
       OLD_HILL_NUMBER               0
       OLD_HILL_STEP               0
       NHILLS_START_VAL               0
       &METAVAR
         SCALE     1.0000000000000000E+00
         COLVAR               1
         &WALL
           TYPE  REFLECTIVE
           POSITION    -1.5707963267948966E+00
           &REFLECTIVE
             DIRECTION  WALL_MINUS
           &END REFLECTIVE
         &END WALL
         &WALL
           TYPE  REFLECTIVE
           POSITION     1.5707963267948966E+00
           &REFLECTIVE
             DIRECTION  WALL_PLUS
           &END REFLECTIVE
         &END WALL
       &END METAVAR
       &PRINT
         &PROGRAM_RUN_INFO  OFF
         &END PROGRAM_RUN_INFO
         &COLVAR  OFF
         &END COLVAR
       &END PRINT
     &END METADYN
   &END FREE_ENERGY
        &PRINT
                &RESTART
                        &EACH
                        MD 20
                        &END EACH
                &END RESTART
&TRAJECTORY
FILENAME thion_dimer-dft-trj.xyz
FORMAT XYZ
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES
LOG_PRINT_KEY T
FORMAT XYZ
&EACH
MD 1
&END EACH
ADD_LAST NUMERIC
&END VELOCITIES
        &END PRINT
&END MOTION
#-------------------------------------------------------------------------------------------------------------------------------------
!&EXT_RESTART
!RESTART_DEFAULT F
!RESTART_FILE_NAME min-thion_dimer-1.restart
!RESTART_POS T
!RESTART_VEL T
!RESTART_THERMOSTAT T
!&END EXT_RESTART

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