events:2016_summer_school:qmmm
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events:2016_summer_school:qmmm [2016/08/25 09:58] – mwatkins | events:2016_summer_school:qmmm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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School of Mathematics and Physics, University of Lincoln, UK | School of Mathematics and Physics, University of Lincoln, UK | ||
- | http:// | + | https:// |
{{https:// | {{https:// | ||
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$$ | $$ | ||
- | Periodic electric field uses the Berry phase formalism of the [[http:// | + | Periodic electric field uses the Berry phase formalism of the [[https:// |
- | {{http:// | + | {{https:// |
- | [[http:// | + | [[https:// |
==== QM/MM ==== | ==== QM/MM ==== | ||
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Well known method is QMMM, one main strand arose from the bio community - aiming to accurately model active sites in proteins | Well known method is QMMM, one main strand arose from the bio community - aiming to accurately model active sites in proteins | ||
- | {{ exercises: | + | {{exercises: |
typically the active site was surrounded by a finite number of classical point charges | typically the active site was surrounded by a finite number of classical point charges | ||
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An attractive feature of CP2K's QMMM implementation is that it can be fully periodic, or anything from a cluster to a 3D system. | An attractive feature of CP2K's QMMM implementation is that it can be fully periodic, or anything from a cluster to a 3D system. | ||
- | {{exercises: | + | {{exercises: |
{{ exercises: | {{ exercises: | ||
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the final term $R_{low} (|\mathbf{r}-\mathbf{R}_a|)$ is the residual part of the function not represented by the Gaussians, and should be rather smooth. | the final term $R_{low} (|\mathbf{r}-\mathbf{R}_a|)$ is the residual part of the function not represented by the Gaussians, and should be rather smooth. | ||
- | {{http:// | + | The number of terms in the sum $N_g$ is set by the input variable '' |
- | [http:// | + | {{https:// |
+ | |||
+ | [[https:// | ||
== Short range electrostatic coupling - collocating the potential == | == Short range electrostatic coupling - collocating the potential == | ||
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</ | </ | ||
- | {{http:// | + | {{https:// |
The short range part is put onto grids in much the same manner as in the GPW method. | The short range part is put onto grids in much the same manner as in the GPW method. | ||
- | [[http:// | + | [[https:// |
== Periodic embedding == | == Periodic embedding == | ||
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section. The default is non periodic embedding. | section. The default is non periodic embedding. | ||
- | {{http:// | + | {{https:// |
+ | |||
+ | [[https:// | ||
+ | |||
+ | == Long range coupling == | ||
+ | |||
+ | has two components | ||
+ | |||
+ | * QM/QM interactions (probably small and maybe not critical) | ||
+ | [[https:// | ||
+ | this is on be default if the periodic keyword is activated | ||
+ | |||
+ | * Residual potential $R_{low}$ is long ranged and can be periodically summed using Ewald techniques. This is on be default if the periodic keyword is activated. | ||
+ | |||
+ | == Coulomb coupling == | ||
+ | |||
+ | Alternatively for Semi Empirical Hamiltonians or DFTB it is possible to use " | ||
+ | |||
+ | Here the field from the classical ions acts on the Gaussian basis functions, much like the efield talked about earlier | ||
+ | |||
+ | < | ||
+ | METHOD QMMMM | ||
+ | @include QS.inc | ||
+ | @include MM.inc | ||
+ | &QMMM | ||
+ | #this defines the QS cell in the QMMM calc | ||
+ | &CELL | ||
+ | ABC 12.6 15.0 12.6 | ||
+ | PERIODIC XZ | ||
+ | &END CELL | ||
+ | ECOUPL COULOMB # use classical point charge method | ||
+ | </ | ||
+ | |||
+ | $$ | ||
+ | V_{ab, | ||
+ | $$ | ||
+ | |||
+ | see this [[https:// | ||
+ | |||
+ | ===== Input files ===== | ||
+ | |||
+ | Example setup for KCl that we used [[https:// | ||
+ | |||
+ | {{https:// | ||
+ | |||
+ | We need to define the whole system as normal | ||
+ | |||
+ | < | ||
+ | & | ||
+ | #this defines the cell of the whole system | ||
+ | #must be orthorhombic, | ||
+ | &CELL | ||
+ | ABC 12.6 100.0 12.6 | ||
+ | &END CELL | ||
+ | & | ||
+ | COORD_FILE_NAME kcl.xyz | ||
+ | COORD_FILE_FORMAT XYZ | ||
+ | & | ||
+ | & | ||
+ | # | ||
+ | LIST 1..48 | ||
+ | & | ||
+ | &END | ||
+ | &END | ||
+ | &KIND K | ||
+ | ELEMENT K | ||
+ | BASIS_SET DZVP-MOLOPT-SR-GTH | ||
+ | POTENTIAL GTH-PBE-q9 | ||
+ | &END KIND | ||
+ | &KIND Cl | ||
+ | BASIS_SET DZVP-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE-q7 | ||
+ | &END | ||
+ | &END SUBSYS | ||
+ | </ | ||
+ | |||
+ | We need a normal section for the QM part | ||
+ | |||
+ | < | ||
+ | &DFT | ||
+ | BASIS_SET_FILE_NAME BASIS_MOLOPT | ||
+ | POTENTIAL_FILE_NAME GTH_POTENTIALS | ||
+ | & | ||
+ | COMMENSURATE # this keyword is required for QMMM with GEEP | ||
+ | CUTOFF 150 | ||
+ | &END MGRID | ||
+ | &QS | ||
+ | EPS_DEFAULT 1.0E-12 | ||
+ | &END QS | ||
+ | &SCF | ||
+ | EPS_SCF 1.0E-06 | ||
+ | MAX_SCF 26 | ||
+ | SCF_GUESS RESTART | ||
+ | &OT | ||
+ | MINIMIZER CG | ||
+ | PRECONDITIONER FULL_SINGLE_INVERSE | ||
+ | &END OT | ||
+ | & | ||
+ | EPS_SCF 1.0E-05 | ||
+ | &END OUTER_SCF | ||
+ | &END SCF | ||
+ | &XC | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | & | ||
+ | & | ||
+ | NLUMO 10 | ||
+ | | ||
+ | & | ||
+ | &END PRINT | ||
+ | &END DFT | ||
+ | < | ||
+ | |||
+ | A MM section | ||
+ | |||
+ | < | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | ATOM K | ||
+ | | ||
+ | &END CHARGE | ||
+ | & | ||
+ | ATOM Cl | ||
+ | | ||
+ | &END CHARGE | ||
+ | & | ||
+ | & | ||
+ | atoms K Cl | ||
+ | A [eV] 4117.9 | ||
+ | B [angstrom^-1] 3.2808 | ||
+ | C [eV*angstrom^6] 0.0 | ||
+ | RCUT [angstrom] 3.0 | ||
+ | &END WILLIAMS | ||
+ | & | ||
+ | atoms Cl Cl | ||
+ | A [eV] 1227.2 | ||
+ | B [angstrom^-1] 3.1114 | ||
+ | C [eV*angstrom^6] 124.0 | ||
+ | RCUT [angstrom] 3.0 | ||
+ | &END WILLIAMS | ||
+ | & | ||
+ | atoms K K | ||
+ | A [eV] 3796.9 | ||
+ | B [angstrom^-1] 3.84172 | ||
+ | C [eV*angstrom^6] 124.0 | ||
+ | RCUT [angstrom] 3.0 | ||
+ | &END WILLIAMS | ||
+ | &END NONBONDED | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | & | ||
+ | EWALD_TYPE spme | ||
+ | ALPHA .44 | ||
+ | GMAX 40 | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | </ | ||
+ | |||
+ | The QMMM section is | ||
+ | |||
+ | < | ||
+ | & | ||
+ | #this defines the QS cell in the QMMM calc | ||
+ | &CELL | ||
+ | ABC 12.6 15.0 12.6 | ||
+ | PERIODIC XZ | ||
+ | &END CELL | ||
+ | ECOUPL GAUSS # use GEEP method | ||
+ | NOCOMPATIBILITY | ||
+ | USE_GEEP_LIB 6 # use GEEP method | ||
+ | & | ||
+ | #in this case QM box = MM box in XZ so turn | ||
+ | #off coupling/ | ||
+ | & | ||
+ | &END | ||
+ | &END PERIODIC | ||
+ | #these are just the ionic radii of K Cl | ||
+ | #but should be treated as parameters in general | ||
+ | #fit to some physical property | ||
+ | & | ||
+ | RADIUS 1.52 | ||
+ | &END MM_KIND | ||
+ | & | ||
+ | RADIUS 1.67 | ||
+ | &END MM_KIND | ||
+ | #define the model | ||
+ | & | ||
+ | MM_INDEX 25..32 41..48 | ||
+ | &END QM_KIND | ||
+ | & | ||
+ | MM_INDEX 17..24 33..40 | ||
+ | &END QM_KIND | ||
+ | &END QMMM | ||
+ | </ | ||
+ | |||
+ | Note the CELL in the QMMM section is not the same size as in the main `& | ||
+ | |||
+ | ==== Multiple force environments ==== | ||
+ | |||
+ | it is possible to create rather interesting effects by combining results from several calculations in some way: | ||
+ | For instance there is an example in `$CP2K/ | ||
+ | |||
+ | A mixed calculation in CP2K will have multiple `FORCE_EVAL` sections | ||
+ | |||
+ | < | ||
+ | & | ||
+ | FORCE_EVAL_ORDER 2 3 | ||
+ | &END | ||
+ | |||
+ | & | ||
+ | | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | |||
+ | & | ||
+ | METHOD QS | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | The default is to have a mapping 1-1 between atom index (i.e. all force_eval share the same geometrical structure). | ||
+ | |||
+ | This can be changed by providing a mapping between atoms in the different force_evals. | ||
+ | |||
+ | See this [[https:// | ||
+ | |||
+ | === Example - subtractive QM/MM === | ||
+ | |||
+ | We can implement very simple subractive QMMM using a mixed force_env that would look schematically like this | ||
+ | |||
+ | < | ||
+ | & | ||
+ | FORCE_EVAL_ORDER 2 3 | ||
+ | &END | ||
+ | |||
+ | & | ||
+ | | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | |||
+ | & | ||
+ | METHOD QS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | ==== Task farming ==== | ||
+ | |||
+ | A final note is that CP2K has quite reasonable task farming capability | ||
- | [[http://pubs.acs.org/ | + | There are some examples in the test directories $CP2K/cp2k/tests/ |
events/2016_summer_school/qmmm.1472119094.txt.gz · Last modified: 2020/08/21 10:14 (external edit)