[CP2K-user] [CP2K:11587] Restraints in MD
Adam
adam.mi... at gmail.com
Tue Apr 23 19:39:54 UTC 2019
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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