Questions about QM/MM excercises
Matt W
MattWa... at gmail.com
Tue Sep 6 08:49:47 UTC 2016
Hi,
if you change the QMMM coupling to Gauss, it needs to use an extra GEEP
library file called MM_POTENTIAL (which I think the error implies it found)
AND it needs you to specify the `USE_GEEP_LIB` variable (to something like
6). This variable tells CP2K how many gaussians to use in expanding the
electrostatic potential of the MM atoms.
Maybe some explanation
here https://www.cp2k.org/events:2016_summer_school:qmmm and in the papers
cited there.
Matt
On Tuesday, September 6, 2016 at 7:56:27 AM UTC+1, Chanwoo Noh wrote:
>
> Hello, I am Chanwoo Noh, and I am a beginner of the CP2K.
> I want to execute QM/MM calculation using CP2K.
> In order to understand the QM/MM calculation, I have studied the exercises
> in CP2K homepage, https://www.cp2k.org/exercises:2015_cecam_tutorial:urea
> In this exercise, urea zwitterion structure is stabilized by classical MM
> method during first and second tasks, and QM/MM isothermal calculation is
> performed in third task.
> The original exercise input uses semi-empirical(SE) method for QM
> calculation, and this input file works very well.
> However, when I do the homeworks, in which semi-empirical method should
> convert to use GPW, I got a following error message from the CP2K output
> file.
>
>
>
> *******************************************************************************
> * ___
> *
> * / \
> *
> * [ABORT]
> *
> * \___/ Radius Value not found in MM_POTENTIAL file *
> * |
> *
> * O/|
> *
> * /| |
> *
> * / \
> qmmm_gaussian_input.F:236 *
>
> *******************************************************************************
>
> As the homework directs, I inserted the multigrid options, reasonable
> basis sets and pseudo potential options in input files, but the error
> message occurs.
>
> I don't know why this problem occur when I just changed the QM option from
> SE to GPW.
> When I use the GPW for QM/MM, should I change the force field parameter or
> other topology file in addition to the input file?
> Anyone helps me, thanks.
>
> For helping your understanding, I copy my input file as follow.
>
>
> @SET ROOT /home/chanwoo/CP2K/QMMM/UREA
> &FORCE_EVAL
> METHOD QMMM
>
> &MM
> &FORCEFIELD
> parm_file_name ${ROOT}/Files/mol_solv.top
> parmtype AMBER
> &SPLINE
> R0_NB [angstrom] 0.1
> RCUT_NB [angstrom] 9.0
> EMAX_SPLINE 10.0
> &END
> &END FORCEFIELD
> &POISSON
> &EWALD
> EWALD_TYPE spme
> ALPHA .4
> GMAX 54
> O_SPLINE 4
> &END EWALD
> &END POISSON
> &END MM
>
> &DFT
> BASIS_SET_FILE_NAME BASIS_MOLOPT #basis folder
> name
> POTENTIAL_FILE_NAME GTH_POTENTIALS
> &MGRID
> #multigrid option
> COMMENSURATE
> CUTOFF 280
> &END MGRID
> &QS
> #GPW option is used.
> METHOD GPW
> EPS_DEFAULT 1.0E-12
> &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 10
> &END
> &PRINT
> &RESTART OFF
> &END
> &RESTART_HISTORY OFF
> &END
> &END
> &END SCF
>
> &XC #exchange
> energy functional option
> &XC_FUNCTIONAL PBE
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
>
> &QMMM
> &CELL
> ABC [angstrom] 20.4199430428 20.5538777943 20.6355827553
> PERIODIC NONE
> &END CELL
> ECOUPL GAUSS #Coulomb Calculation option is
> changed to Gaussian
> &MM_KIND O
> RADIUS 1.5
> &END MM_KIND
> &MM_KIND N
> RADIUS 1.5
> &END MM_KIND
> &MM_KIND C
> RADIUS 1.5
> &END MM_KIND
> &MM_KIND H
> RADIUS 0.8
> &END MM_KIND
>
> &QM_KIND O
> MM_INDEX 8
> &END QM_KIND
> &QM_KIND N
> MM_INDEX 1 6
> &END QM_KIND
> &QM_KIND C
> MM_INDEX 5
> &END QM_KIND
> &QM_KIND H
> MM_INDEX 2 3 4 7
> &END QM_KIND
> &PRINT
> &QMMM_CHARGES
> &END QMMM_CHARGES
> &END PRINT
> &FORCEFIELD
> &NONBONDED
> &LENNARD-JONES
> ATOMS HW N2
> EPSILON [kcalmol] 0.052
> SIGMA [angstrom] 2.42
> RCUT [angstrom] 9.0
> &END
> &LENNARD-JONES
> ATOMS HW N4
> EPSILON [kcalmol] 0.052
> SIGMA [angstrom] 2.42
> RCUT [angstrom] 9.0
> &END
> &LENNARD-JONES
> ATOMS HW O
> EPSILON [kcalmol] 0.058
> SIGMA [angstrom] 2.2612
> RCUT [angstrom] 9.0
> &END
> &END
> &END
> &END QMMM
>
> &SUBSYS
> &CELL
> ABC [angstrom] 20.4199430428 20.5538777943 20.6355827553
> &END CELL
> &TOPOLOGY
> CONN_FILE_NAME ${ROOT}/Files/mol_solv.top
> CONNECTIVITY AMBER
> COORD_FILE_NAME ${ROOT}/Files/mol_solv.crd
> COORDINATE CRD
> &END TOPOLOGY
>
> &KIND O
> #basis and potential define
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q6
> &END KIND
> &KIND C
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q4
> &END KIND
> &KIND N
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q5
> &END KIND
> &KIND H
> BASIS_SET DZVP-MOLOPT-GTH
> POTENTIAL GTH-PBE-q1
> &END KIND
>
> &END SUBSYS
> &END FORCE_EVAL
>
> &GLOBAL
> PRINT_LEVEL LOW
> PROJECT UREA-ZW
> RUN_TYPE md
> &END GLOBAL
> &MOTION
> &MD
> ENSEMBLE NVT
> STEPS 100
> TIMESTEP 0.5
> TEMPERATURE 298
> &THERMOSTAT
> TYPE CSVR
> REGION MOLECULE
> &CSVR
> TIMECON [fs] 50.
> &END
> &END
> &END MD
> &PRINT
> &TRAJECTORY
> &EACH
> MD 10
> &END
> &END
> &END
> &END MOTION
> &EXT_RESTART
> RESTART_FILE_NAME ./UREA.restart
> RESTART_DEFAULT F
> RESTART_POS
> RESTART_VEL
> &END
>
>
>
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