6.1. Overview on ORCA’s Multiscale Implementation

ORCA features five primary methods suitable for diverse applications such as proteins, DNA, large molecules, explicit solvation, and crystalline solids:

All methods integrate seamlessly with other ORCA modules, simplifying the preparation and execution of multiscale calculations.

The multiscale features are optimally connected to all other modules and tools available in ORCA allowing the user to handle multiscale calculations from a QM-centric perspective in a simple and efficient way, with a focus on simplifying the process to prepare, set up and run multiscale calculations. Since version 6.1 ORCA provides an automated tool for setting up QM and active regions, which is described here.

From the input side all methods share a common set of concepts and keywords, which will be outlined in this section. In subsequent sections the different methods are described and further input options are discussed.

6.1.1. Combining Multiscale Features with other ORCA Features

The multiscale features can be used together with all other possible ORCA methods:

  • Single Point Calculations: Use all kinds of available electronic structure methods as QM method.

  • Optimization: Use all kinds of geometry optimizations with all kinds of constraints, TS optimization, relaxed surface scans, and the ScanTS feature. Use the L-Opt and L-OptH features including the combination of all kinds of fragment optimizations (fix fragments, relax fragments, relax only specific elements in fragments, treat a fragment as a rigid body).

  • Transition States and Minimum Energy Paths: Use all kinds of Nudged-Elastic Band calculations Nudged-Elastic Band calculations (Fast-NEB-TS, NEB, NEB-CI, NEB-TS, including their ZOOM variants) and Intrinsic Reaction Coordinate calculations. (not implemented for MOL-CRYSTAL-QMMM and IONIC-CRYSTAL-QMMM)

  • Conformational Searches: Conformational Searches can be run with ORCA’s GOAT module.

  • Frequency Calculations: Use regular frequency calculations. If required, ORCA automatically switches on the Partial Hessian Vibrational Analysis (PHVA) [529] calculation. (not tested for IONIC-CRYSTAL-QMMM)

  • Molecular Dynamics: Use the Molecular Dynamics (MD) module for Born-Oppenheimer MD (BOMD) with QM/MM in combination with all kinds of electronic structure methods. (not implemented for MOL-CRYSTAL-QMMM and IONIC-CRYSTAL-QMMM)

  • Property Calculation: All kinds of regular property calculations are available. For electrostatic embedding the electron density is automatically perturbed by the surrounding point charges.

  • Excited State Calculations: Use all kinds of excited state calculations (TD-DFT, EOM, single point calculations, optimizations, frequencies).

6.1.2. Required Settings for a Multiscale Simulation

In the following, the basic concepts are introduced.

  • QM atoms: The user can define the QM region either directly, or via flags in a pdb file. See QM and Active Region Definition. For an automated buildup

  • of the QM region with miminal user input see here.

  • Active Atoms: The user can choose an active region, e.g. for geometry optimizations the atoms that are optimized, for a frequency calculation the atoms that are allowed to vibrate for the PHVA, or for an MD run the atoms that are propagated. More background is provided here. Input options on how to define the active region in an automated way or in an explicit way are provided below.

A minimal user input for an ONIOM2 type calculation looks like this.

!QM/XTB
%qmmm
  QMCoreAtoms {7 12} end
  ActiveCoreAtoms {7 12} end
end
*xyz 0 1
...

Other aspects that often need to be addressed for multiscale simulations are treated automatically and with reasonable defaults- which can, of course, be controlled by the user. The boundary treatment, i.e. bonds that have to be cut between QM and MM region, and the treatment of overpolarization is covered in the paragraph Boundary Region. Available embedding types are discussed in section Embedding Types. QM2 atoms, which define the low-level region in 3-layer ONIOM calculations, are discussed in section QM2 Atoms.

Detailed information on the different available input and runtime options and additionally available keywords (see Additional Keywords) are given below.

Note

In order to check the multiscale setup done by ORCA, without the need to run the entire simulation, you can invoke the keyword ! QMMMSetup. This makes sure that ORCA stops after the multiscale preparation. The information on the QMMM setup is printed in the output, and a file with the QM region including link atoms is stored (basename_QM.xyz).

6.1.3. QM and Active Region Definition

QM and active region atoms can be defined in three different ways:

  • Explicit definition of all atom indices.

  • Defining the most important atoms (the core atoms) and ORCA determines the full QM and active region.

  • Definition in a pdb file.

6.1.3.1. Explicit Definition of QM and Active Region

The QM and active region can be directly defined in the input as shown in the following example:

%qmmm                  
 QMAtoms {0 1 2 27 28} end      # lists of atoms (counting starts from 0) or
 ActiveAtoms {0:5 16 21:30} end # ranges of atoms (range defined via start:end)
end        
*pdbfile 0 1 ubq.pdb

6.1.3.2. Automated Definition of QM and Active Region

A standard approach in the QMMM scientific literature for defining QM and active regions involves:

6.1.3.2.1. Identifying Important Atoms or Functional Groups

Examples include:

  • Atoms involved directly in bond formation or breakage.

  • Functional groups essential for spectroscopy.

  • Metal ions central to catalytic activities.

  • Entire molecules or ligands binding to proteins.

  • Additional criteria as necessary.

6.1.3.2.2. Including Surrounding Atoms

  • Include all atoms within a defined spatial distance around these important atoms.

6.1.3.2.3. Applying Rules to Avoid Artifacts

Specifically ensure that:

  • The boundary between QM and MM regions cuts through a non-polarized single bond.

  • The topological distance between two QM-MM cuts (the MM gap) is sufficiently large,

  • preventing overly close placement of link atoms.

6.1.3.2.4. Automated procedure in ORCA 6.1

In ORCA 6.1, an automatic scheme has been developed to manage this multistep process. Users specify only key atoms (core atoms) that define the core part of the QM and active regions.

ORCA requires:

  • Knowledge of the system’s topology.

  • Information about functional groups within the system.

Using the newly introduced fragmentation procedure, ORCA automatically determines this information at the start of the calculation. Functional groups are stored as separate fragments based on the user-selected fragmentation procedure.

6.1.3.2.5. Steps of the Automated Procedure (Illustrated for QM Region; analogous steps apply for active regions)

  1. Accept user-defined input QMCoreAtoms.

  2. If QMCore_Type is Fragments, extend QMCoreAtoms to entire fragments, producing an updated QMCoreAtoms set.

  3. Determine all atoms within QMCore_Extension Å around QMCoreAtoms, yielding QMAtoms.

  4. If QMCoreExtension_Type is Fragments, extend QMAtoms to entire fragments, updating the set again.

  5. Include any explicitly user-defined atoms (QMAtoms) in the automatically generated set.

  6. If CheckAutoFragForQMGaps is true, verify no topologically close QM atoms are separated by fewer MM atoms than QMGap_MinLength. If so, add necessary connecting fragments to QMAtoms.

  7. If CheckAutoFragBoundaries is true, ensure that QM-MM boundaries do not cut polarized or problematic bonds.

  8. Repeat steps 6 and 7 until no further fragments need addition.

Note

You can add the keyword QMMMSetup to your input. This allows you to check the autogenerated QM region (basename_QM.xyz) and verify the charge and multiplicity required for the actual multiscale calculation. that is needed for the actual multiscale calculation.

The automated QM and active region setup can be defined in the input as shown in the following example:

! QM/XTB
! QMMMSetup # just do the preparation and stop
%qmmm
 QMCoreAtoms {2032} end
 ActiveCoreAtoms {2032} end
 frag
   FragProc NABackbone, NASideChains, FunctionalGroups, Extend, Connectivity
 end
end

*xyz 0 1
../../_images/qmmm-autofrag_rna.png

Fig. 6.1 QM region for QMCoreAtom 2032. Left is the QM region in ball-and-stick style as part of the full system in cartoon style, right is the QM region with link atoms.

In the above example, which is a ligand bound to RNA, we first define the fragments using the fragmentator) using RNA specific groups and functional groups (for the ligand), and then build the QM and active region around the ligand (atom 2032 is an atom of the ligand).

! QMMMSetup # just do the preparation and stop
! QMMM
%qmmm
  ORCAFFFilename "reactant.ORCAFF.prms"
  QMCoreAtoms {183 2745} end
  ActiveCoreAtoms {183 2745} end
  frag
    FragProc SEQBACKBONE, AASCFINEGRAINED, FUNCTIONALGROUPS, EXTEND, Connectivity
    UseTopology true
    TopolFile "reactant.ORCAFF.prms"
  end
end
*pdbfile 0 1 reactant.pdb
../../_images/qmmm-autofrag_prot.png

Fig. 6.2 QM region for QMCoreAtoms 183 and 2745. Left is the QM region in ball-and-stick style as part of the full system in cartoon style, right is the QM region with link atoms.

In the above example, involving a covalent ligand bound within a protein active site, we first define the fragments using the fragmentator, specifying protein-specific groups and functional groups for ligands and cofactors. We then construct the QM and active regions around the two critical atoms directly involved in the covalent binding process: atom 183 from the Cys reside, and atom 2745 from the covalently binding ligand.

Table 6.1 Options to automatically define the QM and active region.

Keyword

Options

Description

QMCOREATOMS

{ints...}

Defines the core atoms of the QM region. Single indices can be given as int int. Ranges of atom indices can be provided as int:int. All these can be combined.

ACTIVECOREATOMS

{ints}

Defines the core atoms of the active region.

Frag

As defined here

QMCore_Type

Fragments

(Default) Take as QM core the atoms that the user defines plus all atoms of the fragments which they belong to.

Atoms

Take as QM core only the atoms that the user defines.

QMCoreExtension_Type

Fragments

(Default) Take as QMAtoms the atoms that belong to fragments which have at least one atom which has a distance of less than QMCore_Extension to any of the QMCoreAtoms.

Atoms

Take as QMAtoms the atoms that have a distance of less than QMCore_Extension to any of the QMCoreAtoms.

QMCore_Extension

real

Distance by how much the QM core is extended to yield QMAtoms. Default 3.

CheckAutoFragForQMGaps

true/false

Check whether two QM atoms show a QM gap, i.e. which are topologically connected by more than QMGap_MinLength MM atoms and if so, add the connecting fragments to QMAtoms.

QMGap_MinLength

0 to 6

Topological distance between two QM atoms which determines whether the connecting MM atoms are considered as a QM gap. Default 3

CheckAutoFragBoundaries

true/false

Check whether a QM-MM bond is an unpolar single bond. If not, add the MM atom’s fragment to QMAtoms.

ActiveCore_Type

Fragments

(Default) Take as active core the atoms that the user defines plus all atoms of the fragments which they belong to.

Atoms

Take as active core only the atoms that the user defines.

ActiveCoreExtension_Type

Fragments

(Default) Take as ActiveAtoms the atoms that belong to fragments which have at least one atom which has a distance of less than ActiveCore_Extension to any of the ActiveCoreAtoms.

Atoms

Take as ActiveAtoms the atoms that have a distance of less than ActiveCore_Extension to any of the ActiveCoreAtoms.

ActiveCore_Extension

real

Distance by how much the active core is extended to yield ActiveAtoms. Default 5.

CheckAutoFragForQMGaps_Active

true/false

Check whether two active atoms show a gap, i.e. they are topologically connected by more than QMGap_MinLength non-active atoms and if so, add the connecting fragments to ActiveAtoms.

CheckAutoFragBoundaries_Active

true/false

Check whether a active-nonactive bond is an unpolar single bond. If not, add the non-active atom’s fragment to ActiveAtoms.

Note

Automated setup can be combined with explicit definition of QM or active atoms via QMAtoms and ActiveAtoms.

6.1.3.3. Definition of QM and Active Region via pdb file

The QM and active region can be defined in the pdb file as shown in the following example:

%qmmm
 Use_QM_InfoFromPDB true     # get the QMAtoms and ActiveAtoms definition from 
 Use_Active_InfoFromPDB true # the pdb file. The default for both is false.
                             # If InfoFromPDB is set to true, the QMAtoms or 
                             # ActiveAtoms input is ignored
end
*pdbfile 0 1 ubq.pdb

If Use_QM_InfoFromPDB or Use_Active_InfoFromPDB is set to true, a pdb file should be used for the structural input. QM atoms are defined via 1 in the occupancy column, MM atoms via 0. Active atoms are defined via 1 in the B-factor column, non-active atoms via 0.

ubq.pdb:
...
ATOM    327  N   ASP A  21      29.599  18.599   9.828  0.00  0.00      P1   N
ATOM    328  HN  ASP A  21      29.168  19.310   9.279  0.00  0.00      P1   H
ATOM    329  CA  ASP A  21      30.796  19.083  10.566  0.00  1.00      P1   C
ATOM    330  HA  ASP A  21      31.577  18.340  10.448  0.00  1.00      P1   H
ATOM    331  CB  ASP A  21      31.155  20.515  10.048  2.00  1.00      P1   C
ATOM    332  HB1 ASP A  21      30.220  21.082   9.865  2.00  1.00      P1   H
ATOM    333  HB2 ASP A  21      31.754  21.064  10.801  2.00  1.00      P1   H
ATOM    334  CG  ASP A  21      31.923  20.436   8.755  1.00  1.00      P1   C
ATOM    335  OD1 ASP A  21      32.493  19.374   8.456  1.00  1.00      P1   O
ATOM    336  OD2 ASP A  21      31.838  21.402   7.968  1.00  1.00      P1   O
ATOM    337  C   ASP A  21      30.491  19.162  12.040  0.00  0.00      P1   C
ATOM    338  O   ASP A  21      29.367  19.523  12.441  0.00  0.00      P1   O
...

Note

Contrary to the hybrid36 standard of PDB files, ORCA writes non-standard pdb files as:

  • atoms 1-99,999 in decimal numbers

  • atoms 100,000 and beyond in hexadecimal numbers, with atom 100,000 corresponding to index 186a0.

This ensures a unique mapping of indices. If you want to select an atom with an index in hexadecimal space (index larger than 100,000), convert the hexadecimal number into decimals when choosing this index in the ORCA input file. Note also, that in the pdb file, counting starts from 1, while in ORCA counting starts from zero.

6.1.4. Active Atoms in Combination with Optimization, Frequency Calculation, MD

The systems of multiscale calculations can become quite large with tens and hundreds of thousands of atoms. In multiscale calculations the region of interest is often only a particular part of the system, and it is common practice to restrict the optimization to a small part of the system, which we call the active region = active part of the system. For info on how to define the active region see QM and Active Region Definition. Usually this active part consists of hundreds of atoms, and is defined as the QM region plus a layer around the QM region. The same definition holds for frequency calculations, in particular since after optimization non-active atoms are not at stationary points, and a frequency calculation would lead to artifacts in such a scenario. MD calculations on systems with hundreds of thousands of atoms are not problematic, but there are applications where a separation in active and non-active parts can be important (e.g. a solute in a solvent droplet, with the outer shell of the solvent frozen).

Note

If no active atoms are defined, the entire system is treated as active.

Note

The active region definitions also apply to MM calculations, but have to be provided via the %qmmm block.

6.1.4.1. Optimization in redundant internal coordinates

In ORCA’s QM/MM geometry optimization only the positions of the active atoms are optimized. The forces on these active atoms are nevertheless influenced by the interactions with the non-active surrounding atoms. In order to get a smooth optimization convergence for quasi-Newton optimization algorithms in internal coordinates, it is necessary that the Hessian values between the active atoms and the directly surrounding non-active atoms are available. For that reason the active atoms are extended by a shell of surrounding non-active atoms which are also included in the geometry optimization, but whose positions are constrained, see Fig. 6.3. This shell of atoms can be automatically chosen by ORCA. There are three options available:

Table 6.2 Options to extend the active region.

Keyword

Options

Description

EXTENDACTIVEREGION

DISTANCE

(Default) The parameter Dist_AtomsAroundOpt controls which non-active atoms are included in the extension shell, i.e. non-active atoms that have a distance of less than the sum of their VDW radii plus Dist_AtomsAroundOpt are included.

COV_BONDS

All (non-active) atoms that are covalently bonded to active atoms are included.

NO

No non-active atoms are included

The user can also provide the atoms for the extension shell manually. This will be discussed in section Frequency Calculation.

../../_images/QMMM_ActiveRegion.svg

Fig. 6.3 Active and non-active atoms. Additionally shown is the extension shell, which consists of non-active atoms close in distance to the active atoms. The extension shell is used for optimization in internal coordinates and PHVA.

The set of active atoms is called the ‘activeRegion’, and the set of active atoms plus the surrounding non-active atoms is called ‘activeRegionExt’. During geometry optimization the following trajectories are stored (which can be switched off):

Table 6.3 Files containing trajectories during optimization.

Filename

Description

basename_trj.xyz

Entire QM/MM system

basename.QMonly_trj.xyz

Only QM region

basename.activeRegion_trj.xyz

Only active atoms

basename.activeRegionExt_trj.xyz

Active atoms plus extension

The following files are stored containing the optimized structures - if requested:

Table 6.4 Files containing optimized structures.

Filename

Description

basename.pdb

Optimized QM/MM system in pdb file format

basename.xyz

Optimized QM/MM system

basename.QMonly.xyz

Only QM region

basename.activeRegion.xyz

Only active atoms

basename.activeRegionExt.xyz

Active atoms plus extension

6.1.4.2. Optimization with the Cartesian L-BFGS Minimizer

For very large active regions the quasi-Newton optimization in internal coordinates can become costly. It can be advantageous to use the L-Opt or L-OptH feature, see section Geometry Optimizations using the L-BFGS optimizer. In the context of multiscale simulations it can also be useful to treat parts of the system or full molecules of the system as rigid. E.g. you can optimize the hydrogen positions of the protein and water molecules, and at the same time relax non-standard molecules, for which no exact bonded parameters are available, as rigid bodies. For available options in that context see Optimization Assuming a Rigid Body. An example is shown here:

!QMMM L-OptH
%qmmm
 QMAtoms {22397:22423} end
 ORCAFFFilename "DNA_hexamer.ORCAFF.prms"
end
*pdbfile 0 1 DNA_ligand.pdb

%frag 
 Definition
  1 {22307:22396} end # cofactor
  2 {22397:22423} end # ligand
 end
end

%geom 
 RigidFrags {1 2} end # treat cofactor and ligand as individual rigid bodies
end

6.1.4.3. Frequency Calculation

If all atoms are active, a regular frequency calculation is carried out when requesting !NumFreq. If there are also non-active atoms in the QM/MM system, the Partial Hessian Vibrational Analysis (PHVA) is automatically selected. Here, the PHVA is carried out for the above defined activeRegionExt, where the extension shell atoms are automatically used as ‘frozen’ atoms. Note that the analytic Hessian is not available due to the missing analytic second derivatives for the MM calculation. Note that in a new calculation after an optimization it might happen that the new automatically generated extended active region is different compared to the previous region before optimization. This means that when using a previously computed Hessian (e.g. at the end of an optimization or a NEB-TS run) the Hessian does not fit to the new extended active region. ORCA tries to solve this problem by fetching the information on the extended region from the .hess file. If that does not work (e.g. if you distort the geometry after the Hessian calculation) you should manually provide the list of atoms of the extended active region. This is done via the following keyword:

%qmmm
 OptRegion_FixedAtoms {27 1288:1290 4400} end  # manually define the 
                                               # activeRegionExt atoms.
end

Note that ORCA did print the necessary information in the output of the calculation in which the Hessian was computed:

Fixed atoms used in optimizer          ... 27 1288 1289 1290 4400

6.1.4.4. Nudged Elastic Band Calculations

NEB calculations (section Nudged Elastic Band Method) can be carried out in combination with the multiscale features in order to e.g. study enzyme catalysis. When automatically building the extension shell at the start of a Multiscale-NEB calculation, not only the coordinates of the main input structure (‘reactant’), but also the atomic coordinates of the ‘product’ and, if available, of the ‘transition state guess’ are used to determine the union of the extension shell of the active region. For large systems it is advised to use the active region feature for the NEB calculation.

Note

The atomic positions of the non-active atoms of reactant and product and, if available, transition state guess, should be identical.

6.1.4.5. Molecular Dynamics

If there are active and non-active atoms in the multiscale system, only the active atoms are allowed to propagate in the MD run. If all atoms are active, all atoms are propagated. For more information on the output and trajectory options, see section Regions.

6.1.5. Boundary Region

This section is important for the QM/MM, QM/QM2 and QM/QM2/MM methods. For the latter method two boundary regions are present (between QM and QM2 as well as between QM2 and MM region), and both can go through covalent bonds. In the following we will only discuss the concept for the boundary between QM and MM, but the same holds true for the other two boundaries.

6.1.5.2. Bonded Interactions at the QM-MM Boundary

The MM bonded interactions within the QM region are neglected in the additive coupling scheme. However, at the boundary, it is advisable to use some specific bonded interactions which include QM atoms. By default ORCA neglects only those bonded interactions at the boundary, where only one MM atom is involved, i.e. all bonds of the type QM1-MM1, bends of the type QM2-QM1-MM1, and torsions of the type QM3-QM2-QM1-MM1. Other QM-MM mixed bonded interactions (with more than two MM atoms involved) are included. The user is allowed to include the described interactions, which is controlled via the following keywords:

%qmmm
 DeleteLADoubleCounting true     # Neglect bends (QM2-QM1-MM1) and torsions 
                                 # (QM3-QM2-QM1-MM1). Default true. 
 DeleteLABondDoubleCounting true # Neglect bonds (QM1-MM1)
end

6.1.5.3. Charge Alteration

If QM and MM atoms are connected via a bond (defined in the topology file), the charge of the close-by MM atom (and its neighboring atoms) has to be modified in order to prevent overpolarization of the electron density of LA and QM region. This charge alteration is automatically taken care of by ORCA in %qmmm block. ORCA provides the most popular schemes that can be used to prevent overpolarization.

Table 6.5 Options to modify the charge at the QM-MM boundary in order to prevent overpolarization.

Keyword

Options

Description

ChargeAlteration

CS

(Default) Charge Shift - Shift the charge of the MM atom away to the MM2 atoms so that the overall charge is conserved

RCD

Redistributed Charge and Dipole - Shift the charge of the MM atom so that the overall charge and dipole is conserved

Z0

Keep charges as they are. This MM atom will probably lead to overpolarization

Z1

Delete the charge on the MM1 atom (no overall charge conservation)

Z2

Delete the charges on the MM1 atom and on its first (MM2) neighbors (no overall charge conservation)

Z3

Delete the charges on the MM1 atom and on its first (MM2) and second (MM3) neighbors (no overall charge conservation)

Scale_RCD

real

For RCD scheme defines where on the bond between MM1 and MM2 the shifted charge is positioned. Default: 0.5, i.e. midpoint.

Scale_CS

real

For CS scheme defines where on the bond between MM2 and MM1/MM3 the shifted charge is positioned. Default: 0.06 x bond.

6.1.6. Embedding Types

There are two embedding schemes available for treating the electrostatic interaction between high level and low level region. In the electrostatic embedding scheme the electrostatic interaction between QM and MM system is computed at the QM level. Thus, the charge distribution of the MM atoms (or other low level methods) can polarize the electron density of the QM region. The following embeding schemes are available:

Table 6.6 Options for embedding scheme to treat the electrostatic interaction between high and low level region.

Keyword

Options

Description

Embedding

Electrostatic

(Default) The electrostatic interaction between QM and MM system is computed at the QM level.

Mechanical

The electrostatic interaction between QM and MM system is computed at the MM level.

Important

In QMMM the LJ interaction between QM and MM system is always computed at the MM level.

In the scheme of electrostatic embedding, the evaluation of the electrostatic potential generated by the MM part can be accelerated by using the FMM algorithm (described in reference [786]). This will speed up the building of the Fock Matrix. The default recommended setup can be called using the FMM-QMMM keyword directly in the keywords line. However, more details about the algorithm parameters and all input options can be found in (see also paragraph Fast Multipole Method)

! FMM-QMMM

It is recommended to use that option whenever the MM part is composed of more than 10,000 atoms (or point charges for ECM methods).

6.1.7. Additional Keywords

Here we list additional keywords and options that are accessible from within the %qmmm block and that are relevant to QM/MM calculations. Some of these keywords can also be accessed via the %mm block, see section Available Keywords for the MM module.

!QMMM
%qmmm

# The extended active region, activeRegionExt, contains the atoms surrounding the 
# active atoms.
 ExtendActiveRegion distance  # rule to choose the atoms belonging 
                              # to activeRegionExt.
                              # no - do not use activeRegionExt atoms
                              # cov_bonds - add only atoms bonded covalently to 
                              # active atoms
                              # distance (default) - use a distance criterion (VDW 
                              # distance plus Dist_AtomsAroundOpt)
 Dist_AtomsAroundOpt 0.0      # in Angstrom (Default 0). Meaning only freeze atoms
                              # which touch the active atoms by their VDW spheres.
                              # only needed for ExtendActiveRegion distance
 OptRegion_FixedAtoms {27 1288:1290 4400} end  # manually define the
                                               # activeRegionExt atoms.
                                               # Default: empty list. 
                                               
# Printing options. All are true by default.
 PrintLevel 1               # Can be 0 to 4, 0=nothing, 1=normal, ...
 PrintOptRegion true        # Additionally print xyz and trj for opt region
 PrintOptRegionExt false    # Additionally print xyz and trj for extended 
                            # opt region
 PrintQMRegion true         # Additionally print xyz and trj for QM region
 PrintFullTRJ true          # Print trajectory of full system. Default true.
 PrintPDB true              # Additionally print pdb file for entire system, is 
                            # updated every iteration for optimization
 
# Computing MM nonbonded interactions within non-active region.
 Do_NB_For_Fixed_Fixed true # Compute MM-MM nonbonded interaction also for 
                            # non-active atom pairs. Default true.
# Treats all active water molecules that are treated on MM level as rigid bodies 
#  in optimization and MD simulation, see section "Rigid Water".
 Rigid_MM_Water false       #  Default false.

end
                             
*pdbfile 0 1 ubq.pdb  # structure input via pdb file, but also possible via 
                      # xyz file
Table 6.7 Additional keywords in the %qmmm block, which are also accessible from the %mm block.

Keyword

Options

Description

ORCAFFFilename

"<filename>"

Filename of the ORCA Force Field prms file.

Do_NB_For_Fixed_Fixed

true/false

Compute MM-MM nonbonded interaction also within non-active region, i.e. for non-active atom pairs. Default true. For GOAT and Crystal-QMMM default is false.

RIGID_MM_WATER

true/false

Optimization and MD of active MM waters. Default false.

ExtendActiveRegion

distance

Scheme to extend the active region to activeRegionExt. See also here. distance: Use a distance criterion (VDW distance plus Dist_AtomsAroundOpt).

cov_bonds

Add only atoms bonded covalently to active atoms.

no

Do not add any atoms to activeRegionExt.

Dist_AtomsAroundOpt

<real>

Distance to be added to VDW distance for ExtendActiveRegion. In Angstrom. Default 0.

OptRegion_FixedAtoms

{ints}

List of atoms to define the extended active region. Default: empty list.

PrintOptRegion

true/false

Additionally print xyz and trj for opt region. Default true.

PrintOptRegionExt

true/false

Additionally print xyz and trj for extended opt region. Default false.

PrintPDB

true/false

Additionally print pdb file for entire system, is updated every iteration for optimization. Default false.