Jaguar - Counterpoise Panel

The Jaguar - Counterpoise panel allows you to perform the necessary calculations to correct for BSSE in non-covalently-bonded gas-phase complexes.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Quantum Mechanics → Counterpoise
  • Click the Tasks button and browse to Jaguar → Counterpoise
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Molecular Quantum Mechanics → More Molecular QM Tasks → Counterpoise

Jaguar jobs can also be run from the command line. To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see jaguar Command Help. See the Jaguar Command Reference Manual for further information, including a description of the input file.

  • Overview
  • Features
  • Additional Resources
  • Examples

Overview of Counterpoise Calculations

Counterpoise calculations are a way to correct dissociation energies for the finite size of the basis set used.

In a molecule, the basis set for an atom is effectively enlarged by the basis sets on nearby atoms: basis functions on neighboring atoms can fill in the holes in the basis set. The energy that would be calculated for that atom inside the molecule is lowered relative to the isolated atom by the presence of neighboring basis sets. The error due to the difference in basis sets between the molecule and the isolated atoms is called basis set superposition error (BSSE).

So if we calculate the energy of a hydrogen bond by first calculating the energy of the complex, then subtracting the energies calculated for the isolated molecules, we will overestimate the strength of the bond. Counterpoise calculations correct for this overestimation by using the basis set for the entire system for the isolated molecule rather than just the basis set for the isolated molecule itself. Then the molecule benefits from the extra basis functions both in the complex and in isolation, and the effects of the extra basis functions cancel to some extent.

Counterpoise-corrected dissociation energies require several calculations:

  1. Geometry optimization of the complex (or molecule) whose dissociation energy you want to calculate in the basis set of the complex.
  2. Geometry optimization of the fragments in the basis sets of the fragments.
  3. Single-point calculations on the fragments at the geometry of the complex in the basis sets of the fragments.
  4. Single-point calculations on the fragments at the geometry of the complex in the basis set of the complex.

The difference between the first and the second gives the uncorrected dissociation energy. It is the last two that provide the counterpoise correction, which is the difference between the energies from the third and fourth calculations, and is positive.

Jaguar provides the Counterpoise panel for calculation of the counterpoise-corrected dissociation energy of non-bonded complexes. In this panel you can make settings for the basis set, level of theory, SCF convergence, and geometry optimization. You can run multiple complexes, and distribute the calculations over multiple processors. The counterpoise-corrected energy for each complex is calculated and returned.

There is also a panel for calculating energies of hydrogen-bonded complexes, with a specific protocol for the calculations—see the topic HBond Panel for details.

For other types of counterpoise calculations, such as breaking covalent bonds, you will need to set up the input files for the calculations. Jaguar's facility for counterpoise calculations is general, so it can be applied in any situation. To do a calculation on a fragment in the basis of the complex, you use the input file for the complex. The atoms of the complex that are not in the fragment must be identified, which is done by placing an @ character after the atom name in the zmat section, e.g.

Na4@ 0.00000 0.00000 4.00000

This makes the atom a "ghost" atom, i.e. one with no nucleus and no electrons, only a basis set where the atom would otherwise be. Having set up the input files, you will have to run a job for each, and then calculate the counterpoise-corrected dissociation energy from the resulting energies. More information can be found in Counterpoise Calculations.

Jaguar - Counterpoise Panel Features

Tabs
  • Input
  • Theory
  • SCF
  • Optimization

Input Tab Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Defaults tools

These tools allow you to specify the default basis set and the default level of theory.

Theory text box and button

Click the button to select the level of theory. A small pane opens with controls for selecting the level of theory. The pane consists of a search text box, a filter button, and a list of available theoretical models. Typing in the text box narrows the list to items that contain the text. Clicking the filter button allows you to set options to restrict the list to certain models, e.g. range-corrected DFT. When you choose an item from the list, the pane closes and the text box (which is noneditable) shows the level of theory you chose.

Making a choice of functional sets the dftname keyword in the gen section of the input file.

See DFT Keywords in the Jaguar Input File for information on the density functionals.

Basis set text box and button

Click the button to select the basis set. A small pane opens with controls for selecting the basis set. The pane consists of a search text box, a filter button, and a list of basis sets. Typing in the text box narrows the list to basis set names that contain the text. Clicking the filter button allows you to set options to restrict the list to basis sets with certain features: ECP, diffuse functions, pseudospectral, relativistic, RI-MP2 compatible. When you choose a basis set from the list, the pane closes and the text box (which is noneditable) shows the basis set you chose.

If the basis set is not available for any of the structures in the Structures table, the cell in the Basis Set column for that structure is colored red. If a composite method is chosen in the Theory text box, the corresponding pre-defined basis set is automatically selected, and the Basis set text box cannot be modified.

See Basis Sets for information on the basis sets available.

Structures table

This table lists the entries in the Project Table that are used as the input structures for the job, according to the choice from the Use structures from option menu. To change the structures used for the calculation, you can change the selected structures or included structures in the Project Table panel or the Entry List panel. You can double-click in a cell to edit the values (ID, In, and Entry Title columns are not editable). The columns of the table may be different depending on the calculation type, and include:

  • ID—The entry ID of the structure.
  • In—Use this column to display the structures in the Workspace, just as in the Project Table panel or the Entry List panel. If you chose Workspace as the source of structures, excluding structures from the Workspace (clearing the In box) removes them from the table.
  • Entry Title—The entry title of the structure.
  • Charge—Specify the charge (molchg in the gen section). Default is 0 and is displayed in italics. The value is stored as a Maestro property.
  • Spin Mult.—Specify the spin multiplicity (multip in the gen section). Default is 1 (singlet) and is displayed in italics. If you use the spin-orbit ZORA Hamiltonian, spin is no longer conserved, and the multiplicity is only related to the number of electrons (1 for even, 2 for odd). The value is stored as a Maestro property.
  • Theory—Specify the level of theory (dftname in the gen section) for each structure. Double-click in a cell to edit the level of theory. A small window is displayed with controls for selecting the functional. These controls are the same as for setting the default theory (see above), except that functionals that are not available for the molecule are dimmed.
  • Basis set—Specify the basis set (basis in the gen section) for each structure. Double-click in a cell to edit the basis set. A small window is displayed with controls for selecting the basis set. These controls are the same as for setting the default basis set (see above), except that basis sets that are not available for the molecule are dimmed. The tooltip for the cell shows the basis set and the number of basis functions for the structure. If a composite method is chosen in the Theory column, the corresponding pre-defined basis set is used and the cell becomes noneditable.

Theory Tab Features

In this tab, you select options for the level of theory used in the calculation—SCF, DFT, LMP2. The controls displayed in this tab depend on the level of theory selected.

Theory settings for option menu

Select an option from this menu to make settings for the three types of theoretical methods used: Hartree-Fock (HF), density functional theory (DFT), and local second-order Møller-Plesset perturbation theory (LMP2). The controls in the rest of the tab depend on the choice you make from this menu.

SCF and DFT options

Set options for SCF and DFT calculations.

SCF Spin treatment options

The treatment of spin restriction in the SCF process can be controlled by three options.

  • Automatic—run a spin-unrestricted calculation for open-shell systems (multip>1) and a spin-restricted calculation for closed-shell systems (multip=1). Sets iuhf=2 in the gen section.

  • Unrestricted—run a spin-unrestricted (UHF or UDFT) calculation for both closed-shell and open-shell systems. For closed-shell systems this may give the same result as a restricted calculation, but can deviate from it where a single determinant is no longer a good description of the wave function. Sets iuhf=1 in the gen section.

  • Restricted—run a spin-restricted (ROHF or RODFT) calculation for open-shell systems (sets iuhf=0 in the gen section).

These options are only displayed if you choose HF (Hartree-Fock) or DFT (Density functional theory) from the Level of theory option menu. The default is Automatic: unrestricted for open-shell HF or DFT calculations, restricted for closed-shell calculations.

When using the spin-orbit ZORA Hamiltonian, the spin is no longer conserved. Time-reversal symmetry takes the place of spin symmetry, and Kramers restriction takes the place of spin restriction. So choosing Restricted runs a Kramers-restricted SCF calculation (where time-reversal symmetry is imposed), and Unrestricted runs a Kramers-unrestricted SCF calculation.

Excited state controls

Select the Excited state option to perform an excited state calculation using either the time-dependent density-functional method (TDDFT), if the level of theory is DFT, or the time-dependent Hartree-Fock (TDHF) method, if the level of theory is HF. (Note that the option label includes (TDHF) or (TDDFT) to distinguish the two levels of theory.) This option sets itddft=1 in the gen section. For a geometry optimization, this option is labeled Optimize first excited state to indicate that only the lowest excited state is optimized.

The full linear response method is used by default. If you want to use the Tamm-Dancoff approximation, you can choose it from the option menu (itda=1 in the gen section). For TDHF, this corresponds to a configuration interaction singles (CIS) calculation.

The excited states are excitations from a reference state. If the reference state is a closed shell, you can choose whether to generate singlet or triplet excited states, or both, from the Excited state type option menu. (These choices set rsinglet=1 and rtriplet=1 in the gen section). This option menu is not available if you are doing a geometry optimization. If the reference state is a spin-unrestricted open-shell state, all possible spin states that are accessible as single excitations are calculated, but there is no classification of these states by spin. The value of S2 is reported for all states, so you can identify the spin state.

You can calculate excited states with both the scalar ZORA and the spin-orbit ZORA Hamiltonians (see the Hamiltonian option menu). For the scalar ZORA Hamiltonian, all the options are available. The spin-orbit ZORA Hamiltonian generates states of mixed spin, so the Excited state type option menu is not available when you choose this Hamiltonian. You can only use the spin-orbit ZORA Hamiltonian with a closed-shell reference state. This Hamiltonian is useful if you are interested in singlet-to-triplet transitions and phosphorescence lifetimes.

Several settings can be made for the excited state methods, which are only available when you select the Excited state option.

Number of excited states text box

Specify the number of excited states (sets nroot). Note that for a geometry optimization, only the lowest singlet excited state is optimized, regardless of the value in this text box.

You should select more excited states than you are actually interested in, for two reasons. The first is that the initial guess might not accurately reflect the final states, and the second is to ensure that near-degeneracies are accounted for.

Maximum TDHF iterations text box
Maximum TDDFT iterations text box

Specify the maximum number of iterations of the diagonalization procedure (sets mitertd).

Energy convergence threshold text box

Specify the threshold used to determine when the energies of the excited states have converged (sets econtd).

Residual convergence threshold text box

Specify the threshold used to determine when the norm of the residual vector for the excited states has converged (sets rcontd).

The excited state controls are only displayed if you choose HF (Hartree-Fock) or DFT (Density Functional Theory) from the Level of theory option menu.

Grid density option menu

Choose the grid density for the DFT calculation, from Medium, Fine, or Maximum. If you read an input file that contained some other grid density, the grid density is set to Other, otherwise this option is unavailable. If you choose a grid density from this menu, the previous grid density specification is replaced. By default, DFT calculations use grids with a medium point density.

This option menu is only displayed if for DFT methods.

Use 3-body dispersion correction with all applicable dispersion-corrected functionals option

Select this option to include an additional correction for three-body effects for any D3 dispersion-corrected functionals. Only present if you choose DFT (Density Functional Theory) from the Level of theory option menu.

LMP2 Options

Set options for LMP2 calculations. See Local MP2 Settings for more information on the method and its settings.

Core localization method option menu

Choose the localization method for the core orbitals from this option menu.Sets loclmp2c in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) from the Level of theory option menu. The options are:

  • None—Do not localize core orbitals (loclmp2c=0). This is the default.
  • Pipek-Mezey—Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclmp2c=2).
  • Boys—Perform Boys localization (loclmp2c=1).
  • Pipek-Mezey (alt)—Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (loclmp2c=3).
Valence localization method option menu

Choose the localization method for the valence orbitals from this option menu. Sets loclmp2v in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) from the Level of theory option menu. The options are

  • Pipek-Mezey—Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclmp2v=2). This is the default.
  • Boys—Perform Boys localization (loclmp2v=1).
  • Pipek-Mezey (alt)—Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (loclmp2v=3).
Resonance option menu

Choose the handling of resonance structures for aromatic molecules and molecules with conjugated double bonds. Sets ireson in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) or from the Level of theory option menu. The options are:

  • None—Do not delocalize LMP2 pairs over other atoms (ireson=0).
  • Partial delocalization—Delocalize LMP2 pairs over neighboring atoms in aromatic rings (ireson=1).
  • Full delocalization—Delocalize LMP2 pairs over all atoms in aromatic rings (ireson=2).
LMP2 Pairs options

Select the types of LMP2 pairs to include in the calculation. Sets iheter in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) from the Level of theory option menu. The options are:

  • All atom pairs—Treat all atom pairs with LMP2 (iheter=0). This is the default.
  • Hetero atom pairs—Treat atom pairs in which the two atoms are different (except CH pairs) with LMP2 (iheter=1).

RI-MP2 Options

Set options for RI-MP2 calculations. See RI-MP2 Calculations for more information on the method and its settings.

Freeze core option

Select this option to freeze core molecular orbitals (n_frozen_core = -1). The number of orbitals Jaguar freezes by default for each atom is listed here. If this option is not checked, all core molecular orbitals are included in the correlation.

Hamiltonian option menu

For heavy elements, it is necessary to include relativistic effects in the Hamiltonian. In Jaguar there are two ways of doing this: using ECPs, and with an explicit relativistic Hamiltonian. ECPs are handled via the basis set selection. The Hamiltonian option menu allows you to choose the Hamiltonian. The default is Nonrelativistic, which is the usual Schrödinger Hamiltonian. The other choices are for relativistic Hamiltonians, and include (relativistic) in the menu item, to indicate that they include relativistic effects.

  • Nonrelativistic—Use the (nonrelativistic) Schrödinger Hamiltonian. This is the default, and should be used with ECPs. If you choose LMP2 for the level of theory, this Hamiltonian is selected, as LMP2 cannot currently be used with ZORA.

  • Scalar ZORA—Use the scalar ZORA Hamiltonian (relham=zora-scalar or zora-1c in the gen section). This option is only available for single-point HF and DFT calculations. If you choose this option for LMP2, the Level of theory is reset to DFT.

  • Spin-orbit ZORA—Use the spin-orbit ZORA Hamiltonian (relham=zora-so or zora-2c in the gen section). The Hamiltonian includes spin-orbit coupling, which mixes states of different spin and spatial symmetry. Properties are not available with this Hamiltonian. This option is only available for single-point HF and DFT calculations. If you choose this option for LMP2, the Level of theory is reset to DFT.

Both of the ZORA Hamiltonians use a one-center approximation for the ZORA integrals, with the potential taken from the atomic initial guess (potential=local in the relativity section). By default the ZORA integrals are only evaluated for elements with Z > 18; lighter atoms are treated nonrelativistically. You can override this by including a relatom keyword in the relativity section, set to a space- or comma-separated list of elements, e.g. relatom=C N O F.

For ZORA calculations, it is recommended that you choose a heavy-atom basis set that is contracted specifically for ZORA. These basis sets have zora in the name. The dyall-v2z_zora-j-pt-gen basis set is a double-zeta polarized basis set similar to cc-pvdz; the dyall-2zcvp_zora-j-pt-gen basis set adds outer core polarization. Both basis sets are generally contracted, and cover elements up to Rn. There are semi-segmented versions of these basis sets that run faster without loss of accuracy, dyall-v2z_zora-j-pt-seg and dyall-2zcvp_zora-j-pt-seg. The sarc-zora basis set is also of double-zeta quality, and is a segmented contraction, covering elements from La to Rn. For a higher quality, you can use the dyall-3zvp_zora-j-pt-seg and dyall-3zcvp_zora-j-pt-seg basis sets, which are triple-zeta basis sets.

SCF Tab Features

In this tab you set the parameters that control the SCF convergence. Keywords for the gen section of the input file that correspond to the controls in this tab are given in parentheses.

Accuracy level option menu

Set the accuracy for pseudospectral calculations, or turn off the pseudospectral method.

  • Quick— Use mixed pseudospectral grids with loose cutoffs (Sets iacc=3).
  • Accurate— Use mixed pseudospectral grids with accurate cutoffs (Sets iacc=2).
  • Ultrafine— Use ultrafine pseudospectral grids with tight cutoffs (Sets iacc=1).
  • Fully analytic— Perform a fully analytic calculation: turn off the pseudospectral method (Sets nops=1). Can be run in parallel with OpenMP threads—see Running a Multithreaded Jaguar Job with OpenMP.

For more information on grids and cutoffs, see The Grid File for Jaguar Calculations and The Cutoff File for Jaguar Calculations.

Initial guess option menu

Choose the method for generating an initial guess for the molecular orbitals.

  • Atomic overlap—Construct a guess for the molecular orbitals from atomic orbitals (iguess=10). The core orbitals are set to the atomic core orbitals. The overlap matrix is diagonalized in the space of the valence atomic orbitals, and the eigenvectors with the largest eigenvalues are taken for the valence orbitals. The entire set is orthogonalized core first, then valence. This is the default.

  • Atomic density—Construct a guess from a superposition of atomic densities (iguess=11). The density is projected onto the AO basis. The resulting matrix is diagonalized to give natural orbitals, which are used as the initial guess orbitals.

  • Core Hamiltonian—Generate an initial guess by diagonalizing the one-electron Hamiltonian matrix (iguess=0). This is rarely a good guess, as the orbitals are usually too tight.

  • Ligand field theory—For transition metal complexes, use ligand field theory to construct an initial guess for the metal d orbitals. (iguess=25) An effective Hamiltonian is diagonalized, taking into account the assigned formal charges on the metal and the ligand and the occupation of the ligand orbitals, to determine the d-orbitals and the orbital ordering. The core and ligand orbitals are determined from the atomic orbitals using the atomic overlap.

  • Ligand field theory with d-d repulsion—For transition metal complexes, use ligand field theory including d-d repulsion to construct an initial guess (iguess=30). The procedure is the same as above, except that repulsion between the d electrons on the metals is included to determine the orbital ordering and hence the occupation of the d orbitals and the spin state.

Convergence criteria section

In this section you set the criteria for convergence of the SCF process.

Maximum iterations text box

Specify the maximum number of SCF iterations in this text box (maxit). The default value is 48. The absolute maximum allowed is 5000.

Energy convergence text box

Specify the SCF energy convergence threshold in this text box (econv). The default value is 5.0x10-5 Eh.

RMS density matrix change text box

Specify the SCF density convergence threshold in this text box. This value is the maximum change in the RMS density difference between iterations. (dconv). The default value is 5.0x10-6.

Convergence methods section

In this section you choose the methods used to enhance or control convergence.

SCF level shift text box

Specify the level shift for the virtual orbitals (vshift). The default value is 0.0 for non-metallic systems and Hartree-Fock calculations. For DFT calculations on metallic systems the default is 0.2 for hybrid functionals, 0.3 for pure functionals.

Thermal smearing option menu

Select the thermal smearing method for convergence control (ifdtherm). The menu options are:

  • None— Do not use thermal smearing (ifdtherm=0).
  • FON— Fractional occupation number method (ifdtherm=1).
  • pFON— Pseudo-fractional occupation number method (ifdtherm=2).

See the Jaguar User Manual for details of this method.

Initial temperature text box

Set the initial temperature for thermal smearing. (fdtemp in the gen section of the input file). The initial temperature text box is only available if you choose an item other than None from the Thermal smearing option menu.

Convergence scheme option menu

Choose the SCF convergence acceleration scheme (iconv).

  • DIIS— Use the DIIS convergence scheme (iconv=1).
  • OCBSE— Use the OCBSE convergence scheme (iconv=3).
  • GVB-DIIS— Use the GVB-DIIS convergence scheme (iconv=4).
  • Other— Selected if the input file uses another convergence scheme, otherwise unavailable.

For more information on these convergence schemes, see the Jaguar User Manual.

Force convergence option

Attempt to force convergence by adding level shift and decreasing it during iterations, fixing the number of canonical orbitals, and running at ultrafine accuracy (vshift, iacscf=1).

Compute wave function stability option

Perform wave function stability analysis (wf_stability = 1). Eigenvalues of the diagonalized molecular orbital Hessian are reported.

Orbitals section

Set options relating to the orbital occupations, canonicalization, and localization.

Fixed symmetry populations option

Fix the number of electrons in each irreducible representation (ipopsym=1).

Use consistent orbital sets when all input structures are isomers option

When performing calculations on a set of isomers, taken either from the project table or from a file, select this option to ensure that all calculations use the same number of canonical orbitals. This ensures consistency of the calculations and enables the results to be validly compared.

This option is not present in the Jaguar - Reaction panel, as the structures are not isomeric.

Final localization option menu

Choose the localization method for the valence orbitals from this option menu (locpostv).

  • None— Do not localize final valence orbitals (locpostv=0). This is the default.
  • Pipek-Mezey— Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclpostv=2).
  • Boys— Perform Boys localization (loclmp2c=1).
  • Pipek-Mezey (alt) Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (locpostv=3).

Optimization Tab Features

In this tab you set parameters that control the optimization of geometries, and set constraints on geometric parameters in the optimization.

Maximum steps text box

Enter the maximum number of geometry steps to be taken in the optimization. (Sets maxitg.)

Many molecules will meet the convergence criteria after ten or fewer geometry iterations. Input containing very floppy molecules, transition metal complexes, poor initial geometries, or poor initial Hessians may require many cycles to converge.

Switch to analytic integrals near convergence option

When the optimization approaches convergence, switch to using analytic integrals rather than the pseudospectral method. This option is useful for cases where tight convergence is required, as the pseudospectral method may not provide sufficient accuracy. The switch is made when the quantities used to assess convergence are within a factor of 10 of the relevant convergence threshold (sets nops_opt_switch=10; this can be changed in the Edit Job Dialog Box).

Convergence criteria option menu

Set the convergence criteria for geometry optimizations. See Geometry Optimization and Transition-State Keywords in the Jaguar Input File for details of the criteria.

  • Loose—These thresholds are five times larger than the default thresholds. (Sets iaccg=3.)
  • Normal— Set the convergence criteria to the defaults. (iaccg is not set and different defaults are used depending on the system.)
  • Accurate—Set the convergence criteria to the defaults, given in Table 7 in Geometry Optimization and Transition-State Keywords in the Jaguar Input File. (Sets iaccg=2.)
  • Tight—These thresholds are ten times smaller than the default thresholds. (Sets iaccg=5.)
  • Custom—The Energy change, Gradient RMS, and Maximal displacement RMS text boxes are displayed, so you can enter the values you want to use for these criteria.

For optimizations in solution, the default criteria are multiplied by a factor of three, and a higher priority is given to the energy convergence criterion.

Initial Hessian option menu

Choose an initial guess for the Hessian. Sets inhess in the gen section. The choices are:

  • Fischer-Almlof—Use the Fischer-Almlof initial guess. Sets inhess=-1.

  • Schlegel—Use the Schlegel initial guess (the default). Sets inhess=0.

  • Unit Hessian—Use the unit matrix for the initial Hessian. Sets inhess=1.

  • Quantum mechanical—Calculate the Hessian with the given basis set. This is the most expensive but most accurate option, recommended for floppy molecules and other molecules that are difficult to optimize. Sets inhess=4.

  • Other—Read the Hessian from the input file hess section if it exists (see The hess Section of the Jaguar Input File). Otherwise use the default. Automatically selected if the input file has a Hessian, which is the case for restarting a geometry optimization. Sets inhess=2.

Coordinates option menu

Choose a coordinate representation to define the optimization parameters. Sets intopt in the gen section. The ideal set of coordinates is one in which the energy change along each coordinate is maximized, and the coupling between coordinates is minimized. The choices are:

  • Redundant internal—Use internally-generated redundant internal coordinates for the optimization parameters. Sets intopt=1. This is the default, and the most efficient choice in most cases. New coordinates are chosen automatically if a group of atoms becomes collinear.

  • Cartesian—Use Cartesian coordinates for the optimization parameters. Sets intopt=0. Avoids the problems of collinear coordinate sets, but is likely to take longer than for redundant internal coordinates.

  • Z-matrix—Use the Z-matrix from the input file for the optimization parameters. Sets intopt=2. If the geometry input is in Cartesian format or contains a second bond angle rather than a torsional angle for any atom intopt is set to 1. This item is unavailable if you are doing an IRC calculation.

Save intermediate geometries to output structure file option

Save the geometry at each step of the optimization to the output structure file. The structures at each geometry step are imported into Maestro as an entry group. If the geometry optimization fails, you can select one of these structures in Maestro to restart the optimization. Sets ip472=2 in the gen section. You do not need to set this option to inspect the energy convergence, which you can do in the QM Monitor Panel.

Add New Constraint section

Choose a constraint type and pick atoms in the Workspace to define the constraint. When you have picked the required number of atoms for the constraint type, the constraint is listed in the Constraints table. Cartesian constraints are marked with an asterisk in the zmat section; distance, angle, and dihedral constraints are added to the coord section, which is created if it does not exist. You can also choose to add all constraints of a particular type.

Type option menu

Choose the type of constraint. Choices are Cartesian X, Cartesian Y, Cartesian Z, Cartesian XYZ, Distance, Angle, and Dihedral. The Cartesian constraints constrain movement in the specified direction (X, Y, Z, or all three).

Pick option and menu

Choose an object from this option menu, then pick atoms in the Workspace to define the constraint. When you choose from this menu, the Pick option is automatically selected. The available objects are Atoms for Cartesian constraints, and Atoms and Bonds for all other types of constraint. The atoms are marked in the Workspace as you pick them, and each constraint is marked in the Workspace and entered in the Constraints table as it is completed.

Add object button

This button adds all of the specified object type to the constraints table. It is mainly useful when you want to optimize only a small part of a molecule, which you can do by constraining the whole system, then deleting those constraints that you don't want. The button's label and function depend on the choice you make from the Type option menu:

  • Add Selected Atoms—Add the atoms that are selected in the Workspace as constraints. Only available for Cartesian constraints. You can select atoms in the Workspace then click this button to add them to the constraints table.

  • Add All Atom Pairs—Add all atom pairs in the molecule as constraints, whether bonded or not. This choice completely constrains all free parameters, so it is only useful as a first step to removing constraints on the atoms you want to move. Only available for distance constraints.

  • Add All Bond Angles—Add all bond angles in the molecule, i.e. all angles in which the atom at the apex of the angle is bonded to the two other atoms. Only available for angle constraints.

  • Add All Torsions—Add all bonded torsions in the molecule, i.e. all dihedrals defined by three contiguous bonds. Only available for dihedral constraints.

Constraints table

Displays the constraints with their type, and also the target value, if it is a dynamic constraint. You can select one row at at time in the table. The constraint for the selected row is highlighted in the Workspace. You can make a constraint dynamic by entering the desired value in the Target Value column.

You can delete a constraint by selecting it in the table and clicking Delete. To remove all constraints, click Delete All.

Estimated total time text and View details link

Displays an estimate of the total clock-time for the job. Click on the View details link to open the Estimated Total Time Details Dialog Box. For more information, see Timings for Typical Jaguar Jobs.

Keywords text box

Enter keywords and macros for the gen section. These keywords and macros override settings made elsewhere in the panel. They do not appear in the input file when you edit it with the Edit Job Dialog Box, but are added to the gen section when the file is written out on clicking Run. For more information on the keywords you can use, see The gen Section of the Jaguar Input File.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Counterpoise - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Related Topics

Workflow Examples

Example input file (wflow-counterpoise-0001.in):

&gen
basis=6-31G**
igeopt=1
dftname=B3LYP-D3
&
&zmat
O1      0.5716915865187   0.0732238897305  -1.3439923735987
H2      0.2116643326745   0.0677638774030  -0.4009033177849
H3      0.1223156962194  -0.6488136323309  -1.8681076349234
O4     -0.4864929637929  -0.0450897872279   1.1846624700138
H5     -1.1615041564855   0.6139335444371   1.5211579356309
H6      0.0098241613123  -0.4352440882262   1.9622420434721
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run counterpoise.py -jobname=wflow_counterpoise_0001 wflow-counterpoise-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: wflow-counterpoise-0001.in
Output files