[CP2K-user] [CP2K:11587] Restraints in MD

[Adam]

Thanks, Alejandro. Will see if I can get PLUMED to do what I need for this .

Many thanks for this,
Adam

On Tuesday, 23 April 2019 17:36:14 UTC+2, Alejandro Ramos wrote:
>
> Hi,
>
> I didn't understood quite right what you were trying to do, but I would 
> recommend to use Plumed http://www.plumed.org/ to any kind of complex 
> restrained simulation.
>
> Regards,
>
> Alejandro.
>
> El mar., 23 de abr. de 2019 a la(s) 14:22, Adam (ada... at gmail.com 
> <javascript:>) escribió:
>
>> Dear CP2K community,
>>
>>
>> I'm relatively new to CP2K so I apologise for the potentially naive 
>> question. I am having some difficulties getting my restraints to work in MD 
>> calculations and hoping somebody might be able to offer insight. 
>>
>>
>> I am trying to restrain (harmonic restraint) a molecule between a set of 
>> atoms, and observe the change in dynamics of the system. For this, I have 
>> placed a series of ghost atoms, and set restraints between my target 
>> molecule and the ghost atoms. 
>>
>>
>> As a test, I have tried simply to restrain an N2 molecule to a 'surface' 
>> of two atoms. However, as this is a non-linear system, placing the 
>> constraints on the ghost atoms (*i.e. *fixing XYZ of the ghost) leads to 
>> 0 total degrees of freedom (12 - 3 rots - 3 trans - 6 for XYZ ghost 
>> restraints). This doesn't quite reflect what I am trying to achieve, which 
>> is not to constrain the mobility of my molecule, but rather limit the 
>> mobility of a portion of it. 
>>
>>
>> I have therefore been searching for a way to effectively cut the ghost 
>> atoms out of the dynamics itself, and use them only as anchors for 
>> restraints. Unfortunately, I cannot seem to find a way to do this. 
>>
>>
>>
>> Any guidance would be much appreciated!
>>
>>
>> Cheers,
>>
>> Adam
>>
>>
>> =====================
>>
>> &GLOBAL
>>   PROJECT test
>>   PRINT_LEVEL LOW
>>   RUN_TYPE MD
>> &END GLOBAL
>> &FORCE_EVAL
>>   METHOD QS
>>   &DFT
>>     BASIS_SET_FILE_NAME ./BASIS_MOLOPT
>>     POTENTIAL_FILE_NAME ./GTH_POTENTIALS
>>     &MGRID
>>       CUTOFF 300
>>         NGRIDS 5
>>     &END MGRID
>>     &QS
>>        EPS_DEFAULT 1.0E-08
>>        MAP_CONSISTENT
>>        EXTRAPOLATION ASPC
>>        EXTRAPOLATION_ORDER 3
>>     &END QS
>>     &SCF
>>       MAX_SCF 100
>>       EPS_SCF 1.0E-6
>>       SCF_GUESS ATOMIC
>>       &OT ON
>>         MINIMIZER DIIS
>>         N_DIIS 5
>>         PRECONDITIONER FULL_ALL
>>       &END OT
>>         &OUTER_SCF
>>         MAX_SCF 20
>>         &END OUTER_SCF
>>    &PRINT
>>           &RESTART_HISTORY OFF
>>           &END
>>           &RESTART
>>              &EACH
>>                 QS_SCF 0
>>                 MD 1
>>              &END
>>              ADD_LAST NUMERIC
>>           &END
>>     &END
>>     &END SCF
>>     &XC
>>                &VDW_POTENTIAL
>>                 DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>                 &PAIR_POTENTIAL
>>                 TYPE DFTD3
>>                 REFERENCE_FUNCTIONAL PBE
>>                 CALCULATE_C9_TERM .TRUE.
>>                 PARAMETER_FILE_NAME dftd3.dat
>>                 R_CUTOFF 7.0
>>                 &END PAIR_POTENTIAL
>>                 &END VDW_POTENTIAL
>>        &XC_GRID
>>           XC_DERIV SPLINE2
>>        &END XC_GRID
>>       &XC_FUNCTIONAL BLYP
>>       &END XC_FUNCTIONAL
>>     &END XC
>>   &END DFT
>>   &SUBSYS
>>         &CELL
>>         ABC  20.0 20.0 20.0
>>         ALPHA_BETA_GAMMA 90. 90.0 90.0
>>         PERIODIC None
>>         &END CELL
>>         &COORD
>>
>> N -3.6857888996 -1.5575299566 0.0000000000
>>
>> N -3.6552471270 -0.4379381852 0.0000000000
>>
>> H -5.7410666362 -2.5626012324 -0.0000000000
>>
>> H -1.9555182229 -2.6256161365 -0.0000000000
>>         &END COORD
>>     &KIND N
>>       BASIS_SET DZVP-MOLOPT-GTH
>>       POTENTIAL GTH-PBE-q5
>>     &END KIND
>>     &KIND H
>>       GHOST
>>       BASIS_SET none
>>     &END KIND
>>         &COLVAR
>>         &DISTANCE
>>         ATOMS 1 4
>>         &END DISTANCE
>>         &PRINT
>>         &END
>>         &END COLVAR
>>
>>         &COLVAR
>>         &DISTANCE
>>         ATOMS 2 3
>>         &END DISTANCE
>>         &PRINT
>>         &END
>>         &END COLVAR
>>
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>>
>> &MOTION
>>         &CONSTRAINT
>>         SHAKE_TOLERANCE 1.0E-4
>>         &COLLECTIVE
>>         COLVAR 1
>>         INTERMOLECULAR
>>         TARGET [angstrom] 1.000
>>         &RESTRAINT
>>             K 1.0
>>         &END RESTRAINT
>>         &END COLLECTIVE
>>
>>         &COLLECTIVE
>>         INTERMOLECULAR
>>         COLVAR 2
>>         TARGET [angstrom] 1.0
>>         &RESTRAINT
>>            K 1.0
>>         &END RESTRAINT
>>         &END COLLECTIVE
>>
>>         &FIXED_ATOMS
>>            LIST 3
>>         &END FIXED_ATOMS
>>         &FIXED_ATOMS
>>            LIST 4
>>         &END FIXED_ATOMS
>>         &END CONSTRAINT
>>
>>         &MD
>>         ENSEMBLE NVT
>>         STEPS 300
>>         TIMESTEP 0.5
>>         TEMPERATURE 300.0
>> &THERMOSTAT
>>      &NOSE
>>        LENGTH 3
>>        YOSHIDA 3
>>        TIMECON 1000
>>        MTS 2
>>      &END NOSE
>>    &END
>>         &END MD
>>                 &PRINT
>>                 &TRAJECTORY
>>                 &EACH
>>                 MD 1
>>                 &END
>>                 &END
>>                 &VELOCITIES ON
>>                 &END
>>                 &RESTART
>>                 &EACH
>>                 MD 1
>>                 &END
>>                 &END
>>                 &RESTART_HISTORY OFF
>>                 &END
>>                 &END
>> &END MOTION
>>
>>
>>
>>
>>
>>
>>
>>
>>
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