Questions about QM/MM excercises

Matt W MattWa... at gmail.com
Tue Sep 6 10:49:47 CEST 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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