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

[Alejandro Ramos]

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 (adam.mi... at gmail.com)
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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