[CP2K-user] Metadynamics questions, complex continuously moving around low energy position

[Yang Liu]

dear Marcella,

Thanks for your reply! I also realized that the CV remains constant to 1, 
so I should alter the related parameters until it's decreasing to nearly 0, 
right? Then how about the other errors in my input, could you please help 
me point them out? I may not be sensitive enough to find these errors since 
I'm still new to cp2k, thank you so much!

Regards
Yang

On Monday, October 7, 2019 at 7:24:31 PM UTC+9, Marcella Iannuzzi wrote:
>
>
>
> There are several errors in your input, starting from the chosen CV, which 
> is a constant equal 1  according to the given definition. It is a good 
> practice to run not-accelerated MD first to identify the right CVs and 
> related parameters for metadynamics. 
> Regards
> Marcella
>
> On Monday, October 7, 2019 at 7:16:18 AM UTC+2, Yang Liu wrote:
>>
>> dear cp2k users,
>> recently I've been learning metadynamics, and I want to do some work 
>> similar to this image attached, but my complex molecule keeps moving around 
>> low energy position (1) within 4 ps run, instead of moving towards another 
>> cage far from Al as it showed in this image. I would be very grateful if 
>> you could help me solve this problem!
>>
>> [image: 图1.png]
>>
>> here's my input and COLVAR.metadynLog I used,
>>
>>
>>
>>
>> &FORCE_EVAL
>>   METHOD Quickstep
>> @IF ( ${METHOD_TO_USE} == DFT )
>>   &DFT
>>       BASIS_SET_FILE_NAME  ${LIBPATH}/BASIS_MOLOPT
>>       POTENTIAL_FILE_NAME  ${LIBPATH}/GTH_POTENTIALS
>>     &MGRID
>>       NGRIDS 5
>>       CUTOFF 200
>>     &END MGRID
>>     &QS
>>       METHOD GPW
>>       MAP_CONSISTENT
>>       EXTRAPOLATION ASPC
>>       EXTRAPOLATION_ORDER 3
>>     &END QS
>>
>>     &SCF
>>       MAX_SCF 30
>>       EPS_SCF 1.0E-5
>>       SCF_GUESS ATOMIC
>>       &OT
>>         PRECONDITIONER FULL_SINGLE_INVERSE
>>         MINIMIZER DIIS
>>         N_DIIS 7
>>       &END OT
>>
>>       &OUTER_SCF
>>         MAX_SCF 3
>>         EPS_SCF 1.0E-05
>>       &END OUTER_SCF
>>
>>       &PRINT
>>         &RESTART
>>           LOG_PRINT_KEY
>>         &END
>>       &END
>>      &END SCF
>>
>>      &XC
>>       &XC_FUNCTIONAL PBE
>>       &END XC_FUNCTIONAL
>>      &END XC
>>
>>      &POISSON
>>        POISSON_SOLVER MT
>>        PERIODIC NONE
>>        &MT
>>        &END
>>      &END
>>   &END DFT
>> @ENDIF
>> @IF ( ${METHOD_TO_USE} == SE )
>>   &DFT
>>     CHARGE 0
>>     &QS
>>       METHOD PM6
>>       &SE
>>        RC_INTERACTION [angstrom] 50.0
>>        RC_COULOMB     [angstrom] 50.0
>>        RC_RANGE       [angstrom]  0.0
>>       &END
>>     &END QS
>>     &SCF
>>       MAX_SCF 30
>>       EPS_SCF 1.0E-6
>>       SCF_GUESS ATOMIC
>>       &OT 
>>         MINIMIZER DIIS
>>         PRECONDITIONER FULL_SINGLE_INVERSE
>>       &END
>>       &OUTER_SCF
>>         EPS_SCF 1.0E-6
>>         MAX_SCF 5
>>       &END
>>       &PRINT
>>         &RESTART OFF
>>         &END
>>         &RESTART_HISTORY OFF
>>         &END
>>       &END
>>     &END SCF
>>   &END DFT
>> @ENDIF
>>
>> &SUBSYS
>>     &CELL
>>       ABC   11.724228  11.763936  11.722788
>>       PERIODIC XYZ
>>     &END CELL
>>
>>     &TOPOLOGY
>>       CONNECTIVITY  OFF
>>       COORD_FILE ${cp2k_path}/dif_Al/dif_Al_nvt.xyz
>>       COORDINATE XYZ
>>     &END TOPOLOGY
>>
>> @IF ( ${METHOD_TO_USE} == DFT )
>>     &KIND Si
>>       BASIS_SET DZVP-MOLOPT-SR-GTH
>>       POTENTIAL GTH-PBE-q4
>>     &END KIND
>>
>>     &KIND Al
>>       BASIS_SET DZVP-MOLOPT-SR-GTH
>>       POTENTIAL GTH-PBE-q3
>>     &END KIND
>>
>>     &KIND O
>>       BASIS_SET DZVP-MOLOPT-SR-GTH
>>       POTENTIAL GTH-PBE-q6
>>     &END KIND
>>
>>     &KIND H
>>       BASIS_SET DZVP-MOLOPT-SR-GTH
>>       POTENTIAL GTH-PBE-q1
>>     &END KIND
>>
>>     &KIND Cu
>>       BASIS_SET DZVP-MOLOPT-SR-GTH
>>       POTENTIAL GTH-PBE-q11
>>     &END KIND
>>
>> @ENDIF
>>
>>     &COLVAR
>>        &COORDINATION
>>           KINDS_FROM  Cu
>>           KINDS_TO   Al
>>           R_0 [angstrom]  5.03
>>           NN  6
>>           ND  6
>>        &END COORDINATION
>>     &END COLVAR
>>
>>   &END SUBSYS
>>
>> &END FORCE_EVAL
>>
>> &GLOBAL
>>   PROJECT dif_Al_mtd
>>   RUN_TYPE MD
>>   PRINT_LEVEL LOW
>>   WALLTIME 80000
>> &END GLOBAL
>>
>> &MOTION
>>   &MD
>>     ENSEMBLE NVT
>>     STEPS  50000
>>     TIMESTEP 0.8
>>     TEMPERATURE 1173.0
>>     TEMP_TOL   100
>>     &THERMOSTAT
>>       &NOSE
>>         LENGTH 3
>>         YOSHIDA 3
>>         TIMECON 100.0
>>         MTS 2
>>       &END NOSE
>>     &END
>>     ANGVEL_ZERO
>>     COMVEL_TOL  2.0E-7
>>
>>     &PRINT
>>       &ENERGY
>>         &EACH
>>            MD 10
>>         &END
>>       &END
>>
>>       &PROGRAM_RUN_INFO
>>         &EACH
>>            MD 10
>>         &END
>>       &END
>>       FORCE_LAST
>>     &END PRINT
>>   &END MD
>>
>>   &FREE_ENERGY
>>     &METADYN
>>       DO_HILLS
>>       NT_HILLS 100
>>       WW 1.0e-1
>>       LAGRANGE
>>       TEMPERATURE 1173.
>>       TEMP_TOL  10.
>>
>>       &METAVAR
>>     LAMBDA  5
>>         MASS   100.
>>         SCALE 0.3
>>         COLVAR 1
>>         &WALL
>>             POSITION 0.0
>>             TYPE QUARTIC
>>             &QUARTIC
>>                DIRECTION WALL_MINUS
>>                K  100.0
>>             &END
>>         &END
>>       &END METAVAR
>>
>>       &PRINT
>>         &COLVAR
>>            COMMON_ITERATION_LEVELS 3
>>            &EACH
>>              MD 1
>>            &END
>>         &END
>> &HILLS
>>            COMMON_ITERATION_LEVELS 3
>>            &EACH
>>              MD 1
>>            &END
>>         &END
>>       &END
>>     &END METADYN
>>   &END
>>
>>   &PRINT
>>     &TRAJECTORY
>>       &EACH
>>         MD 1
>>       &END
>>     &END
>>     &VELOCITIES OFF
>>     &END
>>     &RESTART
>>       &EACH
>>          MD 100
>>       &END
>>       ADD_LAST NUMERIC
>>     &END
>>     &RESTART_HISTORY 
>>       &EACH
>>          MD 2000
>>       &END
>>     &END
>>   &END
>>   &CONSTRAINT
>>     &FIXED_ATOMS
>>       LIST    5.. 52 55 .. 78
>>     &END
>>   &END
>> &END MOTION
>>
>>
>>
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