Questions about QM/MM excercises

노찬우

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Sep 6, 2016, 2:56:27 AM9/6/16

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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 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 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 MD

&PRINT

&TRAJECTORY

&EACH

MD 10

&END

&END MOTION

&EXT_RESTART

RESTART_FILE_NAME ./UREA.restart

RESTART_DEFAULT F

RESTART_POS

RESTART_VEL

&END

Matt W

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Sep 6, 2016, 4:49:47 AM9/6/16

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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

Chanwoo Noh

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Sep 6, 2016, 5:06:56 AM9/6/16

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Dear Matt W,

Your answer solves the problem. I really thanks for your kind answer.

Chanwoo

Tianshu Jiang in Beijing

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Dec 8, 2017, 2:53:32 AM12/8/17

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Hi, Chanwoo,

I encountered the same problem yesterday, but I have no idea what should be written in MM_POTENTIAL and their meanings.

And what value should be set to variable USE_GEEP_LIB ?

I don't major in chemistry or physics.

I'll appreciate for your reply !

在 2016年9月6日星期二 UTC+8下午5:06:56，Chanwoo Noh写道：

Chanwoo Noh

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Dec 8, 2017, 3:30:03 AM12/8/17

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Dear Tianshu Jiang

I am not an expert, so there may be some mistakes, but I will let you know what I understood.

Original exercise in https://www.cp2k.org/exercises:2015_cecam_tutorial:urea is for the QM/MM method using semi-empirical method.

However, when we use the GPW method instead of semi-empirical method, the additional options also be changed.

1. "ECOUPL COULOMB" should be changed to "ECOUPL GAUSSIAN".

2. "USE_GEEP_LIB 6" option should be inserted in &QMMM.

Here, "USE_GEEP_LIB 6" is the option for using the library in which point charges of MM atoms are approximated as the sum of Gaussians.

The variable of USE_GEEP_LIB is the number of Gaussians used in the approximation.

Therefore, the larger the variable, the higher the accuracy and 6 seems to be adequate.

I recommend you to read the following exercise https://www.cp2k.org/events:2016_summer_school:qmmm .

2017년 12월 8일 금요일 오후 4시 53분 32초 UTC+9, Tianshu Jiang in Beijing 님의 말:

Tianshu Jiang in Beijing

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Dec 8, 2017, 3:55:36 AM12/8/17

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Hi, Chanwoo,

Thanks for your advice. Now I understand the meaning of USE_GEEP_LIB.

I have read the exercise you referred. But there is still something confusing me.

Where should I get the extra GEEP library (referred by Matt in his answer)?

在 2017年12月8日星期五 UTC+8下午4:30:03，Chanwoo Noh写道：

Tianshu Jiang in Beijing

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Dec 9, 2017, 9:02:44 PM12/9/17

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Hi, Chanwoo,

The problem has been solved, I added

NOCOMPATIBILITY

USE_GEEP_LIB 6

in the &QMMM subsection. And then I added

&MGRID

COMMENSURATE .TRUE.

&END

in the &DFT subsection.

Now CP2K run successfully.

在 2017年12月8日星期五 UTC+8下午4:30:03，Chanwoo Noh写道：

Dear Tianshu Jiang

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