Basic Usage of QM/MM in CP2K Pablo Campomanes | CECAM QM/MM School - - PowerPoint PPT Presentation

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Basic Usage of QM/MM in CP2K Pablo Campomanes | CECAM QM/MM School - - PowerPoint PPT Presentation

Feb 02, 2024 238 likes •528 views

Basic Usage of QM/MM in CP2K Pablo Campomanes | CECAM QM/MM School Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond CP2K General Input Syntax Series of blocks (shuffling is allowed, sort them as you

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Basic Usage of QM/MM in CP2K

Pablo Campomanes | CECAM QM/MM School Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond

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CP2K General Input Syntax

Comments can be included: lines starting with # or ! Units can be explicitly included as [UNIT] It is possible to split long lines using \

&SECTION … &END SECTION

Series of blocks (shuffling is allowed, sort them as you like)

&CELL ABC [angstrom] 25.0 25.0 25.0 &END CELL

  • ptional, but recommended
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CP2K Preprocessor directives

@INCLUDE <filename.inc>: The content of the filename.inc file is inserted into the input file and parsed.

Useful to avoid having a very long input file

&FORCE_EVAL &SUBSYS @INCLUDE ‘xyz.inc’ &END SUBSYS &END FORCE_EVAL &COORD O 0.0 0.0 0.0 H 1.0 0.0 0.0 H 0.0 1.0 0.0 &END COORD &FORCE_EVAL &SUBSYS &COORD O 0.0 0.0 0.0 H 1.0 0.0 0.0 H 0.0 1.0 0.0 &END COORD &END SUBSYS &END FORCE_EVAL xyz.inc

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CP2K Preprocessor directives

@SET VAR <value>: Assigns <value> to the preprocessor variable VAR. All occurrences of ${VAR} statement are substituted by the <value> set within the input file.

Useful if you want to set/change a value at multiple places

@SET MD_STEPS 10 &PRINT &TRAJECTORY &EACH MD ${MD_STEPS} &END EACH &END TRAJECTORY &END PRINT &PRINT &TRAJECTORY &EACH MD 10 &END EACH &END TRAJECTORY &END PRINT

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CP2K Preprocessor directives

@IF…@ENDIF: Conditional block. Text inside this block is skipped if expression is equal .false.

Useful for using one input file while keeping multiple run characteristics @SET RUN_TYPE EQUIL &FORCE_EVAL &DFT &QS @IF (${RUN_TYPE} == EQUIL) EPS_DEFAULT 1.0E-10 @ENDIF @IF (${RUN_TYPE} == PROD) EPS_DEFAULT 1.0E-14 @ENDIF &END QS &END DFT &END FORCE_EVAL &FORCE_EVAL &DFT &QS EPS_DEFAULT 1.0E-10 &END QS &END DFT &END FORCE_EVAL

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QM/MM framework in CP2K

Interface region: üQM/MM interactions üCoupling terms MM part: üClassical force field üEnvironmental effects QM part: üDensity Functional Theory

QM/MM with CP2K: modular structure QM and MM on an equal footing (Quickstep + FIST)

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CP2K Input file structure

Four main sections to deal with: &GLOBAL ... &END [GLOBAL] &FORCE_EVAL ... &END [FORCE_EVAL] &MOTION ... &END [MOTION] &EXT_RESTART ... &END [EXT_RESTART]

(kind of simulation to perform & global program parameters ) (description about system & parameters to calculate energy/forces ) (information about MD ensemble used and related parameters) (restart simulation from external input file)

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CP2K Input file structure

Four main sections to deal with: &GLOBAL ... &END [GLOBAL] &FORCE_EVAL ... &END [FORCE_EVAL] &MOTION ... &END [MOTION] &EXT_RESTART ... &END [EXT_RESTART]

(kind of simulation to perform & global program parameters ) (description about system & parameters to calculate energy/forces ) (restart simulation from external input file) (information about MD ensemble used and related parameters)

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&FORCE_EVAL METHOD QMMM (to activate QMMM module) &DFT ... @INCLUDE ‘force_eval_qm.inc’ &END DFT &MM ... @INCLUDE ‘force_eval_mm.inc’ &END MM &QMMM ... (input for QM/MM coupling) &END QMMM &SUBSYS ...

(coordinates, topology, cell)

&END SUBSYS &END FORCE_EVAL

QM/MM calculations: FORCE_EVAL section

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&FORCE_EVAL METHOD QMMM (to activate QMMM module) &DFT ... @INCLUDE ‘force_eval_qm.inc’ &END DFT &MM ... @INCLUDE ‘force_eval_mm.inc’ &END MM &QMMM ... (input for QM/MM coupling) &END QMMM &SUBSYS ...

(coordinates, topology, cell)

&END SUBSYS &END FORCE_EVAL

QM/MM calculations: FORCE_EVAL section

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QM/MM calculations: FORCE_EVAL section

&FORCE_EVAL METHOD QMMM &DFT (info about parameters for QM region) CHARGE 1 (default CHARGE=0) MULTIPLICITY 3 (default MULTIPLICITY=1) UKS (request spin-polarized calc.) BASIS_SET_FILE_NAME ../mypath/BS_filename POTENTIAL_FILE_NAME ../mypath/PP_filename WFN_RESTART_FILE_NAME ../mypath/WFN_filename &QS METHOD GPW (or DFTB/PM6/…) &END QS &XC &XC_FUNCTIONAL PBE (or BLYP/B3LYP/…) &END XC_FUNCTIONAL &END XC ...

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QM/MM calculations: FORCE_EVAL section

&MGRID CUTOFF 320 (density cutoff, in Ry) (equiv. to CPMD wf cutoff=80) &END MGRID &SCF EPS_SCF 1.0E-6 MAX_SCF 50 SCF_GUESS ATOMIC (or RESTART if job cont) &END SCF &PRINT (printing out rho-dependent prop) &MULLIKEN (or LOWDIN charges) FILENAME mypath/mulliken_out_filename &EACH MD 20 &END EACH &END MULLIKEN &END PRINT &END DFT

Other properties that can be printed out: q Molecular orbitals (MO_CUBES) q Total electron or spin density (DENS_CUBE) q And many more… look at the CP2K “manual”

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&FORCE_EVAL METHOD QMMM (to activate QMMM module) &DFT ... @INCLUDE ‘force_eval_qm.inc’ &END DFT &MM ... @INCLUDE ‘force_eval_mm.inc’ &END MM &QMMM ... (input for QM/MM coupling) &END QMMM &SUBSYS ...

(coordinates, topology, cell)

&END SUBSYS &END FORCE_EVAL

QM/MM calculations: FORCE_EVAL section

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QM/MM calculations: FORCE_EVAL section

&MM &FORCEFIELD PARM_FILE_NAME parm.pot PARMTYPE CHM (or G96/AMBER/…) VDW_SCALE14 0.5 EI_SCALE14 0.8333333 &END FORCEFIELD &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &EWALD EWALD_TYPE SPME (or EWALD/PME/…) &END EWALD &END POISSON &END MM

U( r

1,…,

rN ) = ki 2

bonds

∑

r

i − r i, 0

( )

2 +

κ i 2 θi −θi, 0

( )

2 angles

∑

+ Vn 2

torsions

∑

1+ cos nφ +δ

( )

⎡ ⎣ ⎤ ⎦ + + εij σ ij r

ij

⎛ ⎝ ⎜ ⎞ ⎠ ⎟

12

− σ ij r

ij

⎛ ⎝ ⎜ ⎞ ⎠ ⎟

6

⎡ ⎣ ⎢ ⎢ ⎤ ⎦ ⎥ ⎥

pairs

∑

+ 1 4πε

pairs

∑

qiqj r

ij

Loading ff parameters from external file (Ewald summation schemes) (param. controlling LR-electrostatics)

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&FORCE_EVAL METHOD QMMM (to activate QMMM module) &DFT ... @INCLUDE ‘force_eval_qm.inc’ &END DFT &MM ... @INCLUDE ‘force_eval_mm.inc’ &END MM &QMMM ... (input for QM/MM coupling) &END QMMM &SUBSYS ...

(coordinates, topology, cell)

&END SUBSYS &END FORCE_EVAL

QM/MM calculations: FORCE_EVAL section

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QM/MM calculations: FORCE_EVAL section

&QMMM USE_GEEP_LIB 9

(# of gaussians to be used in the expansion of elect. potential)

ECOUPL GAUSS (or NONE/MULTIPOLE/…)

(type of QM/MM elect. coupling)

&CELL !QM box size ABC [angstrom] 25.0 25.0 25.0 &END CELL &QM_KIND C MM_INDEX 1 5

(indexes following MM numbering)

&END QM_KIND &QM_KIND H MM_INDEX 2 3 4 6 7 8 &END QM_KIND &END QMMM

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QM/MM calculations: FORCE_EVAL section

&QMMM USE_GEEP_LIB 9

(# of gaussians to be used in the expansion of elect. potential)

ECOUPL GAUSS (or NONE/MULTIPOLE/…)

(type of QM/MM elect. coupling)

&CELL !QM box size ABC [angstrom] 25.0 25.0 25.0 &END CELL &QM_KIND C MM_INDEX 1 5

(indexes following MM numbering)

&END QM_KIND &QM_KIND H MM_INDEX 2 3 4 6 7 8 &END QM_KIND &END QMMM If covalent bonds between QM and MM regions -> LINK atoms must be added

1 2 3 4 5 6 7 8

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QM/MM calculations: FORCE_EVAL section

&QMMM ... &QM_KIND C MM_INDEX 1 5

(indexes following MM numbering)

&END QM_KIND &QM_KIND H MM_INDEX 2 3 4 6 7 &END QM_KIND &LINK LINK_TYPE IMOMM (H-capping) QM_INDEX 5 MM_INDEX 8 &END LINK &END QMMM

1 5 8

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&FORCE_EVAL METHOD QMMM (to activate QMMM module) &DFT ... @INCLUDE ‘force_eval_qm.inc’ &END DFT &MM ... @INCLUDE ‘force_eval_mm.inc’ &END MM &QMMM ... (input for QM/MM coupling) &END QMMM &SUBSYS ...

(coordinates, topology, cell)

&END SUBSYS &END FORCE_EVAL

QM/MM calculations: FORCE_EVAL section

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QM/MM calculations: FORCE_EVAL section

&SUBSYS (info about the system) &CELL !MM BOX SIZE ABC [angstrom] 80.0 75.0 95.0 PERIODIC XYZ (directions where to apply PBC) &END CELL &TOPOLOGY COORD_FILE_NAME sys.pdb COORD_FILE_FORMAT PDB (or XYZ/G96/…) CONN_FILE_NAME sys.psf CONN_FILE_FORMAT PSF (or AMBER/G96/…) &END TOPOLOGY ...

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QM/MM calculations: FORCE_EVAL section

&KIND O BASIS_SET DZVP-GTH-PBE POTENTIAL GTH-PBE-q6 &END KIND &KIND C BASIS_SET DZVP-GTH-PBE POTENTIAL GTH-PBE-q4 &END KIND &KIND H BASIS_SET DZVP-GTH-PBE POTENTIAL GTH-PBE-q1 &END KIND &END SUBSYS &END FORCE_EVAL

Different basis_set and pseudopotential files can be found in the CP2K distribution

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CP2K Input file structure

Four main sections to deal with: &GLOBAL ... &END [GLOBAL] &MOTION ... &END [MOTION] &EXT_RESTART ... &END [EXT_RESTART]

(kind of simulation to perform & global program parameters ) (description about system & parameters to calculate energy/forces ) (restart simulation from external input file)

&FORCE_EVAL ... &END [FORCE_EVAL]

(information about MD ensemble used and related parameters)

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QM/MM calculations: GLOBAL section

&GLOBAL PRINT_LEVEL MEDIUM (or SILENT/LOW/HIGH/…) PROJECT_NAME MY_PROJECT RUN_TYPE ENERGY_FORCE (or GEO_OPT/MD/…) WALLTIME 86400 ... &END GLOBAL

touch EXIT / touch EXIT_MD

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CP2K Input file structure

Four main sections to deal with: &MOTION ... &END [MOTION] &EXT_RESTART ... &END [EXT_RESTART]

(kind of simulation to perform & global program parameters ) (description about system & parameters to calculate energy/forces ) (restart simulation from external input file)

&FORCE_EVAL ... &END [FORCE_EVAL] &GLOBAL ... &END [GLOBAL]

(information about MD ensemble used and related parameters)

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QM/MM calculations: MOTION section

&MOTION &MD (or GEO_OPT/MC/…) ENSEMBLE NVT (or NVE/NPT/…) STEPS 5000 TIMESTEP 0.5 TEMPERATURE 298 &THERMOSTAT TYPE CSVR (or NOSE/…) &CSVR TIMECON [fs] 50. &END CSVR &END THERMOSTAT &CONSTRAINT ... &END CONSTRAINT &END MD &END MOTION

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CP2K Input file structure

Four main sections to deal with: &EXT_RESTART ... &END [EXT_RESTART]

(kind of simulation to perform & global program parameters ) (description about system & parameters to calculate energy/forces ) (restart simulation from external input file)

&FORCE_EVAL ... &END [FORCE_EVAL] &GLOBAL ... &END [GLOBAL] &MOTION ... &END [MOTION]

(information about MD ensemble used and related parameters)

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QM/MM calculations: EXT_RESTART section

&EXT_RESTART RESTART_FILE_NAME NAME-1.restart RESTART_DEFAULT FALSE RESTART_POS TRUE RESTART_VEL TRUE RESTART_THERMOSTAT TRUE RESTART_AVERAGES FALSE RESTART_COUNTERS FALSE ... &END EXT_RESTART WFN is read if activated in &FORCE_EVAL

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Main CP2K I/O files

Input (required)

cp2k.popt –i NAME.inp –o NAME.out

e.g. NAME.inp (file name and extension are arbitrary)

Optional inputs

POTENTIAL

(pseudopotential library)

BASIS_SET

(basis set library) Topology, coordinates, ff param. (e.g. psf, xyz, pdb…)

@INCLUDE

(files included using preprocessor directives)

Standard outputs

NAME.out

(standard output/log file, not overwritten)

NAME-1.restart

(all info to restart MD / GEO_OPT)

NAME-1.ener

(energies, temperature, conserved Qty)

NAME-1.dcd

(MD trajectory / GEO_OPT steps)

NAME-1.cell

(cell parameters if NPT MD / CELL_OPT)

NAME-RESTART.wfn

(optimized wfn to restart)