List of all keywords

aimnet2_model: string

alpha: float

Exponent in the damping function

amber_amberhome: "N/A"

Configuration: path to base of AMBER installation

amber_auto_gaff: yes | no

amber_auto_gaff_ff: gaff | gaff2

amber_calc_engine: sander | openmm

amber_gbsa: none | lcpo | icosa

Nonpolar (surface-area dependent) energy for generalized Born solvent model. By default, none is used. Available options are:

  • none
  • LCPO - AMBER option gbsa = 1
  • ICOSA - AMBER option gbsa = 2, gradient not available

amber_input_file: string

When specified, user-provided input file (for the sander module) is used, othrevise, cuby is used to build the input. (The input must contain the commands to dump the results and gradient, see the input generated by cuby for reference.)

amber_ld_path: ""

Path to shared libraries used by amber.

amber_leap_commands: ""

Additional commands passed to leap, executed after the system is loaded but before the topology is saved.

amber_leap_disulfide_bridges: yes | no

Automatically add dislulfide bridge bonds between nearby CYX residues.

amber_leaprc: array

A list (array of strings) of leaprc files loaded when prmtop is built automatically. By default, the ff03 and gaff forcefiled are loaded from the $AMBERHOME directory. Each leaprc is preprocessed by cuby and following patterns are replaced with actual paths (to allow easy construction of complex forcefields from different sources):

  • %amberhome (path to amber installation)
  • %home (path to home directory)
  • %cuby (path to cuby inctallation)
  • %pwd (path curernt working directory)

amber_md_thermostat: berendsen | andersen | langevin

Thermostat for MD in amber.

amber_md_thermostat_tc: 0.5

Thermostat coupling constant / collision frequency, in ps.

amber_nb_cutoff: 999.0

Cuttoff for non-bonded interaction. The default value is very large so that all interactions are evaluated.

amber_nb_update: 1

Frequency of update of non-bonded lists. Default is update in every step.

amber_openmm_opt_convlimit: 0.05

Convergence limit for OpenMM optimization (max. element of gradient)

amber_openmm_reference_platform: yes | no

amber_openmm_restraints: array

List of coordinate/angle restraints, in format similar to the one used in the restraints interface

amber_opt_convlimit: 0.01

Convergence limit for geometry optimization in AMBER. Evaluated as root-mean-square of the Cartesian elements of the gradient, in kcal/mol/A.

amber_pbsa: none | sasa | cavdisp

Nonpolar energy for Poisson-Boltzman model. By default, none is used. Available options are:

  • none
  • SASA - AMBER options inp = 1, use_sav = 0
  • CAVDISP - AMBER options inp = 2, use_sav = 1

amber_sander_exe: "$AMBERHOME/bin/sander"

Configuration: path to sander executable. By default, it is taken from AMBERHOME directory, but this can be overriden manually.

amber_sander_exe_mpi: string

Configuration: path to parallel sander executable. Not set by default.

amber_top_file: string

When specified, user-provided topology file is used, otherwise cuby calls leap to generate it

amber_zero_dihedral_fc: yes | no

Set force constants for dihedrals to zero. This is achieved by modification of the topology file.

amberparm_action: ligand_params | fix_protein | fix_protein_keep_h

ani_exe: ""

atom_energy_corrections: hash - a list of name: value pairs

Energy correction (in kcal/mol) applied to each atom of given element.

atomic_charges: mulliken | nbo | esp | spatial | loewdin | becke | hirshfeld | hirshfeld_fragment | forcefield | voronoi_dd | becke_dd

Method of atomic charges calculation:

  • Mulliken - Mulliken charges
  • NBO - Natural Bond Orbital analyis
  • spatial - spatial population analysis (deMon only)
  • loewdin - Loewdin population analysis (deMon only)
  • becke - Becke cell population analysis (deMon only)
  • hirshfeld - Hirshfeld population analysis using reference density of neutral atoms (deMon only)
  • hirshfeld_fragment - Hirshfeld population analysis using reference fragment density (deMon only)
  • forcefield - charges read from forcefield, MM methods
  • voronoi_dd - Voronoi deformation density (deMon only)
  • becke_dd - Becke deformation density (deMon only)

atomic_charges_cap: hash - a list of name: value pairs

Cap charges on selected elements at maximum/minimum value. The excess charge is redistributed according to keyword atomic_charges_cap_redistribute.

atomic_charges_cap_redistribute: neighbours | molecule

atomic_charges_corrections: hash - a list of name: value pairs

Atomtype-specific charge corections

atomic_charges_read: string

File with atomic charges for the whole system (used for electrostatic embedding). If not provided, cuby attempts to obtain the charges from the MM interface (might not be supported by every interface).

atomic_charges_write: string

Name of the file to write the atomic charges to. If not set, the charges are only printed but not saved to a file.

atomic_charges_write_format: charge_list | charges_only | mol2 | pdb

atomic_charges_write_pch: string

Write the charges in the format of point charges with coordinates (x,y,z,charge). The value of the keyword should be a name of the file, nothing is written if the keyword is not set.

auxiliary_basis_mp2: string

Auxiliary basis for RI or density fitting in MP2. Default basis set is used when this keyword is not set and the extrenal program can determine it automatically.

auxiliary_basis_mp2_elements: hash - a list of name: value pairs

Specification of other auxiliary basis set for selected elements. The format is a hash element: "basis_name"

auxiliary_basis_scf: string

Auxiliary basis for RI or density fitting in DFT/HF. Default basis set is used when this keyword is not set and the extrenal program can determine it automatically.

auxiliary_basis_scf_elements: hash - a list of name: value pairs

Specification of other auxiliary basis set for selected elements. The format is a hash element: "basis_name"

balloon_dir: ""

Path to the Balloon program used for building of geometries from SMILES notation.

basisset: string

AO basis set name

basisset_elements: hash - a list of name: value pairs

Specification of other basis set for selected elements. The format is a hash element: "basis_name"

basisset_file: string

User-provided basis set definition in a file. If not defined, the default set of basis set of the program is used. Following locations are searched:

  • Calculation directory

basisset_harmonics: program_default | spherical | cartesian

The form of basis set harmonics. By default, the chice is left to the external program (where it can be e.g. different for difefrent basis sets). This keyword allows enforcing the form if it is supported.

basisset_zeta: integer

Basis set cardinal number, required i.e. for extrapolations.

block_flag: ""

Flag for marking a block in the input (for development purposes).

bond_selection: string

Selection of one bond in the system, provided as two atom selection separated by semicolon.

bsse_correction: yes | no

Swithes on counterpoise correction for basis set superposition error.

bsse_correction_3b: none | full

Counterpoise correction:

  • none - no correction
  • full - all calculations in trimer basis

calculation_print_lookup: yes | no

  • Result of this calculation is printed in a form useable by the lookup interface. The result contains
  • also the contribution from the addplied modifiers.

cdft_constraints: array

Definition of the cDFT constraints, Array (each item defines one constraint) of Hashes with following opions:

  • type: string, either charge or spin
  • target: target value, float
  • selection: cuby selection expression
  • donor: boolean, used to label donor in coupling calculations (optional)
  • donor: acceptor, used to label acceptor in coupling calculations (optional)

cdft_hda: yes | no

Enables electron transfer coupling in cDFT calculations, two constraints with flags 'donor' and 'acceptor set to true must be present

cfour_bin_dir: ""

cfour_bin_dir_mpi: ""

cfour_force_mrcc: yes | no

Use MRCC even for CCSD(T)

cfour_genbas_file: "GENBAS"

Cfour basis set file. It uses ACES2 format and is usually named GENBAS.

cfour_keywords: string

Add extra keywords (in the CFOUR input format) to the input file

cfour_ld_path: ""

Path to libraries used by CFOUR, added to LD_LIBRARY_PATH before the program is executed.

cfour_mrcc_bin_dir: ""

charge: 0

Molecular charge - required for all QM calculations. If not set, a default value 0 is used but a warnig is printed.

charge_from_atomic_charges: yes | no

Calculate monomer charges from atomic charges (the geometry must be read from a file containing atomic charges)

charge_from_file: string

Set the value of the keyword 'charge' with a value read from a file. Now applicable only to XYZ, PDB, SDF and TXT files. When using "charge_from_file", this value can be added to the charge read from the file.

charge_from_file_add: 0

When using "charge_from_file", this value can be added to the charge read from the file.

charmm_dftb_pb_a: hash - a list of name: value pairs

Charge-dependent PB solvation model - parameter A for each element

charmm_dftb_pb_b: hash - a list of name: value pairs

Charge-dependent PB solvation model - parameter B for each element

charmm_exe: "N/A"

Path to the charmm executable

charmm_exe_mpi: "N/A"

Path to the parallel charmm executable (or a script that sets up the MPI environment and then runs charmm)

charmm_extra_stream_files: array

Additional stream files to be applied before the calculation.

charmm_extras: ""

Extra options for charmm, included directly into the input file before the actual calculation.

charmm_extras_gen: ""

Extra options for charmm, included directly into the input file. Unlike the charmm_extras, this keyword aplies only to the generation of the PSF file

charmm_ff_par: string

Forcefield definition file: parameters

charmm_ff_paths: array

Array of paths under which forcefield data (.rtf, .prm, .str) are searched if full path is not provided.

charmm_ff_top: string

Forcefield definition file: topology

charmm_psf_file: string

Path to a charmm PSF file prepared by charmm. The geometry used for the calculation must be identical to the one described by the PSF file. When this kayword is not set, charmm will attempt to generate the PSF file automatically.

charmm_segment_end_patches: hash - a list of name: value pairs

Pathes applied to terminal residues of each segment. The format is a hash with entries "segment_name: start_patch, end_patch". If a segment is not found in this keywors, autodetection of peptide chain ends is attempted (using NTER and CTER patches), otherwise no patches are applied.

charmm_stream_files: array

Load stream file(s) with parameters.

condition: string

Condition that triggers the use of a conditional block. Every conditional block must contain this keyword. The string is evaluated as ruby code.

confgen_balloon_ga: yes | no

Switch for balloon's genetic algorithm conformer search.

confgen_n: 10

Number of conformers to be generated

confgen_random_seed: integer

Random seed passed to the conformer generator (supported by balloon)

confgen_rmsd: 1.0

Target minimum geometry difference between the conformers

connectivity_tolerance: 1.1

Scaling factor for covelent radii used when evaluating connectivity from geometry. In most places in the code, the default value can not be changed, this keyword works only in the Geometry protocol.

connector_angle: 30.0

Out of plane / out of axis displacement (in degrees) for connector types out_of_plane and in_plane.

connector_distance: "vdw"

Distance of teh connector from an atom. Acceptable values are "vdw", "covalent" and a number (distance in A).

connector_orientation: string

Selections (semicolon-separated) defining the coordinate frame for the connector. Three centers (A, B, C) have to be defined for most connector_type values and one center for connector_type apex.

connector_type: linear | perpendicular | out_of_plane | in_plane | apex

Connector orientation with respect to the molecular coordinate frame. The linear/perpendicular/out_of_plane/in_plane connecors are defined as connected to center A, in frame of axis AB and plane ABC provided in the connector_orientation keyword. For out_of_plane and in_plane orientations, displacement angle is provided by keyword connector_angle. The value 'apex' places the connector in the axis of all bonds the atom is involved in, pointing outwards.

coordinates: cartesian | z-matrix | redundant

Coordinate system used for geometry optimization. To use z-matrix, the geometry must be loaded from a z-matrix format.

correlation_convergence: 7

Convergence threshold for iterative calculations of correlation energy, set to 10^-X a.u.

correlation_frozen_core: yes | no

Frozen core for correlation energy calculations

cosmo_rs_params: bp_svp_am1 | bp_tzvp_cosmo | bp_tzvpd_fine

COSMO-RS parameter set. All parametrizations use DFT with BP functional, only the basis sets differ: def-SVP, def-TZVP and def2-TZVPD. Selecting the bp_tzvpd_fine option switches on better algorithm for the construction of the cavity for which these parameters were developed.

ct_scan_interval: array

Interval for scanning the axis between the molecules for the best divider plane. Format is [start, step, end]

cuby_local_data_dir: "~/.cuby4_data"

Path to directory where cuby stores local data (e.g. cache). The directory must be writeable by user.

cuby_threads: 1

Number of calculations executed by cuby in parallel.

cycle_files: string

Expression selecting files to be cycled on

cycle_header_before_run: yes | no

Print cycle header before the job is run (useful only for serial jobs).

cycle_keyword: symbol

Name of the keyword whose value is changed (may be omitted if cycle_templates is used).

cycle_list: array

Array of the values to cycle over

cycle_print_mode: numbers | simple | nothing | full

Mode of printing scan results:

  • numbers - just a column(s) of numbers are printed
  • simple - one result per line, with some description
  • nothing - no printing at all
  • full - Verbose output from the child protocol. Only this option is available for all protocols.

cycle_series_end: float

End of the cycle series

cycle_series_start: float

Start of the cycle series

cycle_series_step: 1.0

Step used to generate the series

cycle_templates: hash - a list of name: value pairs

The iterated value can be used within a string value of a keyword, either alone or in combination with using cycle_keyword (e.g. when changing basis set, change also the name of file it is read from). The hash takes form keyword:template. Character '%' in the template is replaced by the value.

cycle_type: list | series | files | geometry

Values of the paramtere can be either taken from a list (provided in cycle_list) or generated as a series. The 'files' option allows listing files using wildcards (taken form cycle_files).

d3_3body: yes | no

Add 3-body term

d3_3body_scaling: 1.0

d3_3body_sr: 1.333333

d3_a1: float

Parameter a1 for Becke-Johnson damping function

d3_a2: float

Parameter a2 for Becke-Johnson damping function

d3_alpha6: 14.0

Exponent in damping function in C6 term

d3_alpha8: float

Exponent in damping function in C8 term. If if not setm value of d3_alpha6 + 2 is used.

d3_c6_scaling: hash - a list of name: value pairs

Elementwise scaling factors applied to the C6 coefficients

d3_cutoff: 0.0

Distance cutoff for pairwise dispersion terms. The dispersion is switched off smoothly between this value (r) and r + d3_cutoff_buffer A. When set to 0, no cutoff is used (default).

d3_cutoff_buffer: 2.0

Width of the region where dispersion is smoothly swithed off when cutoff is used.

d3_damping: bj | zero | op | cso | tt | erf | bjr0 | bjvdw | none

Selection of damping function:

  • bj (default): the Becke-Johnson damping
  • zero: the original damping function that gets to zero at r = 0
  • op: Optimized-power damping by the M. Head-Gordon group
  • cso: The C-six-only method from the T. Schwabe group
  • tt: Tang & Toennies damping, uses the same parameters as BJ
  • erf: error-function based damping originally used for DFT-SAPT
  • none: no damping

d3_data_patch: string

Patch for dispersion element data, in format identical to the main data file.

d3_disable_c6_extrapolation: yes | no

Fix for systems with atoms with valence number significantly higher than in the molecules used to derive the C6 coefficients.

d3_hh_fix: yes | no

Hydrogen-hydrogen repulsion term for semiempirical methods. Provide parameters using the d3_hh_para keyword.

d3_hh_fix_version: 1

Value 2 switches to new, stronger repulsuion correction

d3_hh_para: hash - a list of name: value pairs

Parameters for the H-H repulsuion correction for SQM methods. Should contain theree parameters, k, e and r0.

d3_hybridization: grimme | grimme_mod | fixed | zero | custom

Hybridization used to determine atomic parameters:

  • grimme: Grimme's continuous hybridization
  • grimme_mod: EXPERIMENTAL modification of Grimme's continuous hybridization
  • fixed: Fixed hybridization based on bond counting
  • zero: use only atomic C6 coefficients
  • custom: provide values using the d3_hybridization_custom keyword

d3_hybridization_custom: array

Custom values for hybridization numbers used for calculation of geometry-dependent C6 coefficients

d3_op_beta: float

Parameter beta for the OP damping

d3_parameter_file: "dispersion3_parameters.yaml"

Name of the file containing default parameters for specific method setups. By default, the parameter file from the interface disrectory is used. Multiple files can be provided as a comma-separated list, if absolute path is ommited, they are searched in current directory and interface directory.

d3_print: pairwise_energies (list, more items can be selected)

d3_r0_scaling: hash - a list of name: value pairs

Elementwise scaling factors applied to the atomic radii used in the damping function

d3_s6: 1.0

Scaling of the C6 term

d3_s8: float

Scaling of the C8 term

d3_scaling: 1.0

Scaling factor for the whole dispersion energy

d3_sr6: float

Radii scaling for damping function in C6 term

d3_sr8: 1.0

Radii scaling for damping function in C8 term

d3_version: default | d3m

Version of the D3 pareametrization.

  • The default is the parametrization from the original Grimme's papers, or from the papers where additional functional/basis set combinations were parametrized.
  • D3M is a reparametrization of the BJ damping for some functionals by Smith et al. (DOI: 10.1021/acs.jpclett.6b00780)

dataset: string

Name of the dataset definition file

dataset_add_ref_to_result: string

Data from the alternative refernce to be added to the result of calculation. The expression is evaluated in ruby, variables corresponding to alternative reference data names can be used.

dataset_from_files: string

Used when dataset = from_files. List of files to build the dataset from. Shell-like wildcards are allowed.

dataset_from_files_job: "energy"

Used when dataset = from_files. Protocol to be aplied to the items in the data set, 'energy' is the dafault.

dataset_from_files_reference: string

Used when dataset = from_files. File to read reference values from. It should be a table with lines formatted as "geometry_file_name reference_value". When not set, zeroes are used.

dataset_group_separator: ""

Separator between groups in the printed table. By default, no separator is used.

dataset_long_numbers: yes | no

Print dataset statistics with more decimals

dataset_plot_columns: 4

Number of columns of plots for dataset_save_plots = gnuplot_tiled.

dataset_plot_extra: hash - a list of name: value pairs

Add extra series to the plots from yaml files. The value should be a hash "name": filename.yaml

dataset_plot_methodname: "calculation"

Name of the current method to be used in plots.

dataset_plot_scale_zero: yes | no

Force the Y axis of the plots to include zero

dataset_plot_x: ""

Label of the x axis in the plots.

dataset_plot_y: ""

Label of the y axis in the plots.

dataset_plots_fn: "dataset_plots"

Name of the file containing the plots, in cases all plots are written to a single file (gnuplot_tiled and yaml format). Corresponding suffix is added automatically.

dataset_print: table | stats | stats_rel | stats_groups | stats_curves | results_array | references | correlation (list, more items can be selected)

List of things to be printed in the output:

  • table - table of results for each item in the data set
  • stats - statistics, in kcal/mol
  • stats_rel - statistics, relative errors in %
  • stats_groups - brief statistics for each group of items
  • stats_curves - statistics along dissociation curves (if applicable)
  • results_array - calculated results as an array for use in dataset file
  • correlation - correlation coefficient and related measures

dataset_processing: none | relative_to_average | relative_to_group_average | relative_to_min | relative_to_group_min

Processing of the results before valuation of the errors (the same transformation is applied also to the reference values).

  • relative_to_average - values are made relative to the average in the whole data set
  • relative_to_group_average - values are made relative to the average in each group
  • relative_to_min - values are made relative to the system with the lowest reference value
  • relative_to_group_min - values are made relative to the system with the lowest reference value in each group

dataset_reference: "default"

A set of reference values to be used. Some data sets might provide alternative data, which can be selected by their name in the data set file. There are three special vaues of this keyword:

  • default - use the 'default' reference data, these are usually the ones from the first publication on the data set
  • best - use the best reference available (it may not be the default one but some that was publised later) if it is provided in the data set file
  • zero - set all reference values to zero

dataset_save_plots: none | text | gnuplot | gnuplot_script | gnuplot_tiled | yaml

For dataset containg plottable series, the plots can be saved as text files (x, y_ref, y_calc) or plotted as image using gnuplot. The gnuplot_tiled options composes the plots into one large image using imagemagick (named dataset_plots.png). Number of colums is defined by keyword dataset_plot_columns.

dataset_select_elements: "all"

Selection of entries by elements. Supports expressions 'all', 'no_more_than(list)', 'at_least_one(list)' and 'at_least_all(list)' where list is comma-separated list of element names.

dataset_select_group: ".*"

Selection of data set entries by group (regexp pattern)

dataset_select_name: ".*"

Selection of data set entries by name (regexp pattern)

dataset_select_tag: ".*"

Selection of data set entries by their tags (regexp pattern)

dataset_short_names: yes | no

Use short names for dataset items

dataset_skip_group: string

Negated selection of data set entries by group (regexp pattern). Applied only when the keyword is used. The entries are first selected using dataset_select_group, then those matching dataset_skip_group are removed.

dataset_skip_name: string

Negated selection of data set entries by name (regexp pattern). Applied only when the keyword is used. The entries are first selected using dataset_select_name, then those matching dataset_skip_name are removed.

dataset_skip_tag: string

Negated selection of data set entries by tag (regexp pattern). Applied only when the keyword is used. The entries are first selected using dataset_select_tag, then those matching dataset_skip_tag are removed.

dcdftb_buffer: 5.0

Default buffer radius (in Angstrom). It is also the default value in the DC-DFTB-MD program.

dcdftb_corrections: none | d2 | d3 | d3bj | d3h4 | d3h5

Corrections for non-covalent interactions implemented in the DC-DFTB-MD code

dcdftb_cubesize: 5.0

Default size (in Angstrom) of the cubic grid used to partition the system. It is also the default value in the DC-DFTB-MD program.

dcdftb_dc: yes | no

Switch the divide and conquer algorithm on (default) or off.

dcdftb_exe_openmp: "N/A"

Configuration: path to the OpenMP DC-DFTB-MD executable

dcdftb_exe_serial: "N/A"

Configuration: path to DC-DFTB-MD executable

dcdftb_fragments: auto | pdb_residues

Algorithm for the fragmentation of the system.

  • Auto - the default mode in DC-DFTB-MD using a grid of cubes.
  • Pdb_residues - each fragments corresponds to a residue in the input PDB file (this is provided by Cuby).

default_interfaces: hash - a list of name: value pairs

Dictionary for automated selection of interfaces for specified method

delete_large_files: yes | no

Delete large files created by the calculation (e.g. data needed to restart a QM calculation) after the job finishes. The output file containing the results is always kept.

delete_temp_files_on_fail: yes | no

Delete large temporary files when the job fails.

demon_auxis_file: ""

Path to the deMon auxiliary basis file (AUXIS)

demon_basis_file: ""

Path to the deMon basis file (BASIS)

demon_call_mpi: yes | no

When set (default), cuby calls mpirun for parallel execution of demon. Otherwise, the parallel executable (or a script doing the mpi setup) is called directly with the number of processors as an argument.

demon_cdft_deformation_density: yes | no

To be used with Voronoi or Becke population constraint to get the e.g. Voronoi Deformation Density scheme.

demon_cdft_force_convergence: yes | no

demon_cdft_phase: alpha | beta

Enforce specific orbital phase convention in cDFT coupling (HDA) calculations. Applies only to development version with cDFT.

demon_cdft_start: 0

SCF error below which cDFT is activated

demon_cdft_tolerance: integer

Constrained DFT tolerance

demon_charges_pol: yes | no

Add polarizability information to external charges (under development)

demon_constrained_dft: none | mulliken | becke | loewdin | hirshfeld_fragment | hirshfeld_atomic | voronoi | spatial | voronoi_dd | becke_dd

Constrained DFT (cDFT). Available population schemes are:

  • none - no cDFT
  • spatial - uses popukation defined in -->demon_spatial_population

demon_cuby_options: ""

Additional options added to the CUBY keyword when modified demon is used.

demon_ecps_file: ""

Path to the deMon effective core potential file (ECPS)

demon_env_setup: ""

Additional commands to set up the environment for running demon.

demon_exe: ""

Path to the deMon executable

demon_exe_mpi: ""

Path to the parallel (MPI) deMon executable

demon_ffds_file: ""

Path to the deMon force field file (FFDS)

demon_fragment_count: integer

Number of fragments, required when calculations uses them

demon_fragment_guess: yes | no

Construct initial guess from DFT calculations of fragments. The fragments must be defined in the input.

demon_keywords: ""

Additional keywords passed directly to deMon.

demon_lib_dir: ""

Path to a directory containing libraries needed to run the deMon executable

demon_maxl_auxis: integer

Maximum L number of auxiliary basis functions during SCF. For deMon version 4.2.5 and above.

demon_mcps_file: ""

Path to the deMon model core potential file (MCPS)

demon_mpirun: "mpirun -np"

MPI wrapper used to run demon in MPI mode.

demon_no_scf: yes | no

If set, energy is calculated on the initial guess of density, no SCF iterations are performed

demon_orbitals: spherical | cartesian

Orbitals used: spehrical or cartesian

demon_plane_axis_a: string

Setup for spatial population analysis: first atom/selection defining the axis of the plane separator

demon_plane_axis_b: string

Setup for spatial population analysis: second atom/selection defining the axis of the plane separator

demon_plane_ratio: float

Setup for spatial population analysis: ratio dividing the distance between atoms A and B

demon_spatial_population: plane_divider

Population scheme dividing the space by a plane. Three parameters should be provided: first reference atom, second reference atom and a ratio

demon_version: ""

demon_with_cuby_interface: yes | no

Set when a modified version of demon with special cuby support is used.

density_convergence: 7

Density convergence threshold for scf, set to 10^-X a.u.

density_fitting: none | scf | correlation | both

Density fitting (or RI approximation) for SCF (DFT or HF) and correlation. Applied only when the code and method support it. Auxiliary basis sets must be set as needed (using auxiliary_basis_scf and auxiliary_basis_mp2).

development: hash - a list of name: value pairs

This keyword is for development purposes only, it makes it possible to temporarily add keywords without defining them explicitly.

dft_grid: coarse | medium | fine | ultrafine | custom

Grid for DFT calculations. The value is translated to an appropriate setup for a specific DFT program by cuby. When value 'custom' is used, a grid specified by keyword 'dft_grid_custom' is passed directly to the program.

dft_grid_custom: string

Custom DFT grid specification in the format used by the intrfaced program.

dft_sapt_level: 3

DFT-SAPT level:

  • 1 = Coulomb + Exchage
  • 2 = 1 + Induction
  • 3 = 2 + Dispersion

dft_sapt_nl_exch: float

Amount of nonlocal exact exchange in hybrid DFT-SAPT calculations. When density fitting is used, it is set to zero. When density fitting is not used, the default value from the functional is used unless it is set by this keyword.

dft_sapt_shift_a: float

DFT-SAPT shift for molecule A

dft_sapt_shift_b: float

DFT-SAPT shift for molecule B

dftb_3rd_order_full: yes | no

Full 3rd order calculation, when disabled, only diagonal (aka. on-site) contribution is calculated. Requires DFTB+ ver 1.2.1

dftb_blur_charges: 0.0

Half-width of gaussian blur of external point charges. Zero for normal point charges.

dftb_cm3_charges: yes | no

Use CM3 charges in SCC. Available only in modified version of the old DFTB program.

dftb_cpe: none | cpe(q)

CPE polarization for DFTB3, requires development version of the DFTB+ code. The method is described in Christensen et al., J. Chem. Phys 143, 084123 (2015).

dftb_d3: yes | no

D3 dispersion as available in DFTB+ since version 17.1.

dftb_d3_hhrep: yes | no

Activates the H-H repulsion used in the D3H4 and D3H5 corrections.

dftb_data_file: string

Path to a file containing data needed by some DFTB calculation (dispersion parameters, spin constants etc.) By default, the data file from the interfacedirectory is used, but this keyword can be used to specify another file.

dftb_dispersion: yes | no

Original dispersion correction as implemented in DFTB+

dftb_do_scc: yes | no

By default, SCC-DFTB calculation is performed. Non-SCC calculation can be invoked by setting this keyword to false.

dftb_e_temp: 0.0

Electronic temerature

dftb_exe: "N/A"

Configuration: path to dftb executable (original program, not DFTB+)

dftb_extra_input_hamiltonian: ""

Extra input for DFTB+ in its native input format, inserted into the Hamiltonian block

dftb_h5: yes | no

Activates the H5 hydrogen bond correction (now available only in development version of DFTB+).

dftb_h5_element_params: hash - a list of name: value pairs

Elementwise parameters for the H5 correction. Default values are the ones published for DFTB3/3OB.

dftb_h5_rscale: 0.714

Parameter for the H5 correction. Default value is the one published for DFTB3/3OB.

dftb_h5_wscale: 0.25

Parameter for the H5 correction. Default value is the one published for DFTB3/3OB.

dftb_hubbard_derivs: dftb3 | old | custom

3rd order DFTB uses derivatives of Hubbard parameter. The default values are those obtained from DFT calculation. The keyword can have following values:

  • dftb3 - use the default parameters for DFTB3/3OB (default)
  • old - an old set of parameters used previously with the MIO set, previously default in Cuby
  • custom - use keyword dftb_hubbard_derivs_custom to provide custom values

dftb_hubbard_derivs_custom: hash - a list of name: value pairs

Values of custom Hubbard derivatives - see keyword dftb_hubbard_derivs.

dftb_kpoints: "0 0 0 1"

Definition of k-points and weights in the format used by DFTB+ (see the manual for details, only the explicit specification is supported). The default value specifies a single point with weight 1.

dftb_safe: yes | no

Use more robust eigensolver

dftb_scc_convergence: 1.0e-05

Self-consistent charges calculation convergence limit (a.u.)

dftb_scc_cycles: 199

Maximum naumber of SCC cycles

dftb_scc_mixer_weight: 0.2

Mixing parameter in the SCC convergence accelerator. Setting it to lower than default value may fix convergence issues but increases the number of SCC cycles.

dftb_slko_basepath: "N/A"

Configuration: path to directories containing the sets of Slater-Koster files

dftb_slko_format: string

Configuration: template for Slater-Koster file naming (where X and Y are elements, upper or lower case). If not present, name of the first file from the slko directory is used as a template.

dftb_slko_set: "N/A"

Configuration: Name of the Slater-Koster parameter file set (name of directory in dftb_slko_basepath)

dftb_use_dftbplus: yes | no

Use DFTB+ program (the interface supports also original DFTB)

dftb_xh_damping: yes | no

XH electrostatic interaction damping to improve hydrogen bonds. Requires DVTB+ ver 1.1

dftb_xh_damping_exp: 4.95

parameter (exponent) for -->dftb_xh_damping . Default value is taken from paper on the method optimized for use with MIO set.

dftbplus_exe: "N/A"

Configuration: path to dftb+ executable

dftd3_exe: ""

dftd4_custom_s6_s8_a1_a2: array

dftd4_exe: ""

dftd4_lib_dirs: ""

Path to libraries needed by the binary, colon separated

dispersion_elements_c: hash - a list of name: value pairs

Override c6 coefficients (unit: same as in the data file, J/nm)

dispersion_elements_r: hash - a list of name: value pairs

Override element radii from the database with custom values (in Angstrom)

dispersion_hyb: yes | no

Use hybridization-dependent parameters

dispersion_mix: jurecka | jurecka_safe | grimme

Mixing of vdW eadii and C6 cooefficient in dispersion calculation. The default parameters must be used with Jurecka's mixing. The safe version uses simpler mixing for elements for which the effective number of valence electrons is not known (i.e. is zero).

dispersion_pm7_cutoff: yes | no

Use a damping and cutoff for long-range contributions as used in PM7. Enable this (along with setting the appropriate parameters) to emulate the dispersion corerction that is built into PM7.

electric_field: array

Homogenous external electric filed. Enetered as a cartesian vector (array), in a.u.

electrostatics_model: point_charges | gaussian | slater

Model for the electrostatic interaction. By default, point charges are used. Diffuse electron distribution can be used as well (Gaussian or Slater monopoles), the distribution widths (atom sizes) are calculated using Hubbard parameters from DFTB parameter set 3OB (experimental, only some elements supported).

element_energies: hash - a list of name: value pairs

Input of energies of free atoms (in kcal/mol)

element_match_condition: at_least | exactly | no_more_than | some_from

Condition applied to matching element list. Possible values:

  • at_least - matches molecules containing all listed elements and possibly others
  • exactly - matches molecules consisting of all listed elements but not more
  • no_more_than - matches molecules that contain some of the listed elements but not these outside the list
  • some_from - matches molecules containg at lest one element from the list

element_match_list: list of symbols

List of elements to be matched.

energy: float

General keyword for input of energy (in kcal/mol)

existing_calc_dir: stop | recreate | reuse | read_results

Handling of calculation directories when existing one is found:

  • stop - program reports the existing directory and stops
  • recreate - old directory is deleted and new is generated
  • reuse - old directory is reused, new input for the external program is not generated
  • read_results - no calculation is run, old results are read

expand_series_template: ""frame_#{'%03d' % i}.xyz""

File name template for the expand_series action. The string is evaluated as ruby expression, variable 'i' (counter starting at 0) can be used.

explicit_correlation: none | f12

Explicit correlation method.

extension_lib_dirs: array

Paths to be passed to the compiler for building the extensions. It is needed only when libraries from non-standard locations are used (e.g. those built by the user in his home directory).

extrapolate_cbs_corr_weight: 1.0

Weight of the higher-order correction, 1.0 by default.

extrapolate_cbs_correction: yes | no

Use higher-order correction (delta CCSD(T)) added to MP2/CBS extrapolated correlation.

extrapolate_cbs_grad_mode: use_mp2_gradient_components | separate_calculations

Mode of gradient calculation:

  • use_mp2_gradient_components - uses four calculations, the MP2 calcuations must yield the gradient components
  • separate_calculations - Correlation gradients calculated from separate MP2 and HF calculations

fireball_d3: yes | no

fireball_data_dir: "N/A"

fireball_dipoles: yes | no

fireball_exe: "N/A"

fireball_keywords: ""

fireball_lib_dir: "N/A"

fireball_params: "Fdata"

fno_occ_tolerance: 1.0e-06

Occupancy threshold for selcction of FNO orbitals. The default value is identical to the default in Psi4.

forcefield_angles: array

Definition of forcefield terms for angles between covalent bonds

forcefield_bonds: array

Definition of forcefield terms for covalent bonds

forcefield_distances: array

Any atom pair, function of distance

forcefield_init: "[]"

User ruby code run at initialization

forcefield_init_step: "[]"

User ruby code run before each step

forcefield_nonbonded: array

Definition of forcefield terms for nonbonded pairs (all but bonds)

forcefield_nonbonded_strict: yes | no

Use more strict criteria for non-bonded pairs

forcefield_torsions: array

Definition of forcefield terms for torsions

fragmentation_cut_bonds: array

Bonds to be cut, used when fragmentation_mode = cut_bonds. Array of entries in the format "atom_selection; atom_selection; d_ratio", d_ratio being the ratio between length of the bond to a hydogen cap atom and the original bond length. The gradient is very sensitive to this, ratio of distances optimized with the method used are needed.

fragmentation_dimer_file: "dimers.pdb"

File to which the geometries of fragment dimers are saved. If set to empty string, no file is generated.

fragmentation_geometry_only: yes | no

If set, the program is aborted after preparation of the fragments but before the calculations are prepared. This is useful for generating the geometries of the fragments for the use in other calculations.

fragmentation_mode: cut_bonds | selections

Mode of fragmentation:

  • cut_bonds - build the fragments by cuting user-defined bonds and all non-covalent contacts.
  • selections - user-defined fragments specified by the keyword fragmentation_selections

fragmentation_monomer_file: "fragments.pdb"

fragmentation_monomer_names: numbers | original | downcase

fragmentation_order: first | second

The default is second-order expansion where the interaction between fragments is treated as pairwise and the link atoms are properly subtracted. The first-order scheme is only for special use, it is applicable only to fragments that are not covalently bound and the interaction between the fragments is neglected.

fragmentation_selections: array

freesasa_exe: "freesasa"

Path to external program freesasa ( used for surface area calculations.

freq_displace_negative: yes | no

Build a new geometry displaced in all modes with negative frequencies

freq_group_rotation: yes | no

Identify negative modes corresponding to a rotation of a small functional group (now supported: methyl) and prepare a geometry displaced in all these modes

freq_mode_scan: yes | no

Save scans (in .xyz format) along all normal modes.

freq_mode_scan_batchsize: 1000

Large multidimensional scans can be split to multiple files, this number specifies number of geometries per file.

freq_mode_scan_e: 10.0

The range scanned is specified by energy (by default, in multiples of the fundamental vibration frequency, this can be changed by keyword freq_mode_scan_e_unit).

freq_mode_scan_e_unit: fundamental_frequency | cm | kcal

Energy unit for keyword req_mode_scan_e. The options are:

  • fundamental_frequency - difefrent range for each mode, in multiples of v0
  • cm - same range for all modes, in cm^-1
  • kcal - same range for all modes, in kcal/mol

freq_mode_scan_grids: array

Grid specification (in dimensionless normal coordinates) for each mode in a multidimensional scan (optional, if not set, the energy-based displacement is used). Two possible formats are available:

  • "seq(start, step, end)" - generates a equally-spaced grid
  • yaml array - an arbitrary list of numbers

freq_mode_scan_multidimensional: array

Multi-dimensional scan in selected modes. If the list of modes is empty, 1D scans for each mode are done instead.

freq_mode_scan_n: 21

Number of points per mode.

freq_molden_file: "vibrations.molden"

Write file for visulatiozation of the vibrations in molden.

freq_print: mode_zpve | reduced_mass | force_constants | transformation (list, more items can be selected)

List of extra features to be printed:

  • mode_zpve - Print ZPVE (in kcal/mol) for each mode
  • reduced_mass - Print the reduced mass of each mode
  • force constants - Print the force constant of each mode
  • transformation - Transformation matrix from normal to cartesian coordinates

frozen_core_elements: hash - a list of name: value pairs

Set custom frozen core for each element. When not set, turbomole's default is used. When set, values for all elements must be provided.

functional: string

DFT functional, in the format recognized by cuby. It is automatically translated to teh format used by the interfaced program. Value 'custom' forces cuby to pass the value of the 'functional_custom' keyword to the program without translation.

functional_custom: string

Custom DFT functional specification in the format used by the intrfaced program.

functional_custom_type: lda | gga | meta_gga | hybrid | meta_hybrid | double_hybrid | range_separated

Type of the custom functional (required in some cases where the calculation setup depends on this). For functionals recognized by cuby, the type is determined automatically.

gamess_exe_version: "00"

GAMESS executable version, the default value '00' should work for a normal installation.

gamess_extra_input: hash - a list of name: value pairs

User modifications for the games input. It is a hash where the key refers to the input block (e.g. SCF for block $SCF) and the value is an arbitrary string inserted into that block. If the block is not built by cuby, it is added with only the provided contents.

gamess_fmo: yes | no

Switches on the Fragment Molecular Orbitals method

gamess_fmo_auto_charge: yes | no

Automatic determination of charge for amino acid residues in protein. For other residues, charges can be defined using keyword gamess_fmo_res_charge.

gamess_fmo_cut_bonds: array

gamess_fmo_frag_charge: hash - a list of name: value pairs

List of fragment charges (fragment number: charge), fragments not on the list are considered neutral.

gamess_fmo_res_charge: hash - a list of name: value pairs

gamess_pcm_radii: hash - a list of name: value pairs

If set, non-default radii are used for PCM. Provide radii in Angstrom for each selection of atoms, no scaling is applied to the radii.

gamess_pcm_radii_add: hash - a list of name: value pairs

Define PCM radii for elements that do not have default values. The radii provided here are scaled by the default facor of 1.2.

gamess_rungms: "N/A"

Path to the gamess "rungms" script.

gaussian_bin_dir: ""

Path to the gaussian binaries directory

gaussian_checkpoint: none | binary | text

Save checkpoint file

gaussian_driver_exe: "N/A"

Path to the gaussian executable. It should be a script that sets up the environment for gaussian and runs it in foreground. The script should produce an output file with suffix .log from an input file (suffix .com) passed as an argument.

gaussian_driver_job: ""

Job specification, in the gaussian format (e.g. "opt" for optimization, "freq" for frequencies etc.) This is used to construct the input.

gaussian_external_output: string

When set, cuby writes the results also in a form readable by gaussian when it is used as a driver for external calculations (see Supported by protocols Energy, Gradient and Hessian.

gaussian_extra_block: ""

Additional block (or blocks, separated by new line) of gaussian input inserted into teh constructed input after the geometry.

gaussian_keywords: ""

Extra keywords in Gaussian format to be appended to the method specification line

gaussian_run_gdma: yes | no

Run the GDMA distributed multipole analysis on the Gaussian output (requires a separte tool)

gaussian_scratch_dir: "/tmp/g09_$$"

Path to the gaussian scratch directory

gaussian_version: ""

Gaussian version, e.g. "g09" - the version name should correspond to the name of the program binary.

gdma_exe: "gdma"

Full path to the GDMA executable

gdma_rank: 2

generated_scan_filename: ""

File used to save the generated geometries (.xyz file)

geo_clustering_fit: nothing | translation | trans_rot

Fitting procedure in measuring the RMSD between geometries in clustering.

geo_clustering_reorder: yes | no

Apply topology-based reordering to the geometries in the clustering. This affects only the similarity calculations, but not the resulting geometries which are not changed.

geo_clustering_representative: closest_to_avg | lowest_energy

geo_clustering_rmsd: 1.0

Similarity threshold for clustring (RMSD, in Angstroms).

geo_clustering_write: representatives | clusters | averages | representatives_series (list, more items can be selected)

geo_filter_energy: float

geometries_action: list | rmsd_matrix | clustering_rmsd | energy_filter_relative | conf_entropy | cat

geometries_in: string

Files to be processed

geometries_out: "processed_geometries"

Directory for processed geometries. It it does not exist, it will be created.

geometry: string

Starting geometry. Can be specified inline in the input in cuby's format or as a name of external file in a format recognized by cuby.

geometry2: string

Secondary geometry used by some actions

geometry_action: none | cat | expand_series | partial_pdb_update | move_closest_contact_vdw_dist | selection_to_atomlist | pdb_renumber | pdb_selection_as_chain | pdb_rename_residues | pdb_renumber_molecules | pdb_charge | pdb_sort_residues | distribute_charge | connect | order_random | order_topo | order_molecules | order_template | rmsd_fit | rmsd_fit_subset | rmsd_fit_reorder | differences | diff_as_geo | diff_as_selection | topologic_ranks | atomtypes | atomtype_bonds | atomtype_angles | build_zmat | zmat_update | moments_of_inertia | element_list | element_counts | element_match | atomization_energy | add_connector | set_connector_dist | sort_mol_by_distance | print_valence | print_center | randomize | random_translation | randomize_intermolecular | center | standard_orientation | orient | rotate_around_bond | rotate_xyz | symmetry | symmetrize | checksum | close_contacts | molden | get_info | list_hbonds | displacement_in_zmat | series_energy_minimum | list_nc_hbonds | list_nc_sigmahole_bonds | list_nc_closest_vdw | update_charges | sum_charges | sdf_check | sum_site_charges

Action to be performed on the geometry in addition to the standard geometry processing:

  • none - do nothing special
  • cat - concatenate geometry and geometry2
  • expand_series - expands multiple-geometry file into frames
  • partial_pdb_update - update coordinates of matching atoms from geometry2 (atom number, atom name, residue number and residue name must be the same)
  • move_closest_contact_vdw_dist - find closest contact between two molecules and move them to vdW distance along this vector
  • selection_to_atomlist - expands a complex selection to list of atoms
  • pdb_renumber - fix numbering of atoms and residues in PDB file
  • pdb_selection_as_chain - sets chain to 'pdb_set_chain' to atoms in 'geometry_action_selection'
  • pdb_rename_residues - set residue names for selected parts of the system as defined in 'pdb_rename_residues'
  • pdb_charge - calculate charge of the system (for proteins only)
  • distribute_charge - distribute charge (read using charge keyword) evenly to all atoms and save it as atomic charge
  • connect - connect two molecules with dummy atom connectors
  • order_random - reorders atoms randomly
  • order_topo - reorders atoms to unique order determined by topology; if there are chemically equivalent atoms, some geometric information is used. Does not work for molecules with high symmetry.
  • order_molecules - reorders atoms so that individual molecules are listed one after another
  • order_template - reorders the atoms to match geometry provrded as geometry2 (using topological analysis)
  • rmsd_fit - translate/rotate geometry so that the RMSD to geometry2 is minimized
  • rmsd_fit_reorder - translate/rotate geometry so that the RMSD to geometry2 is minimized, reordering the molecule first to match topology of molecule 2 (eliminates rotamers)
  • differences - print differences in atom positions
  • diff_as_geo - select atoms from geometry whose position differ from geometry2 by more than position_difference_threshold
  • diff_as_selection - print selection of atoms whose position differ from geometry2 by more than position_difference_threshold
  • atomtypes - print cuby atomtypes
  • atomtype_bonds - prints list of all bonds, atom types involved and bond distance
  • atomtype_angles - prints list of all angles, atoms and atom types involved
  • build_zmat - build Z-matrix from cartesian coordinates
  • zmat_update - update Z-matrix using coordinates from another geometry (geometry2)
  • moments_of_inertia - print principal moments of inertia
  • element_list - print a list of elements in the molecule
  • element_counts - print a list of elements in the molecule and their counts
  • element_match - check for presence/absence of elements, see keywords element_match_list and element_match_condition
  • atomization_energy - atomization energy calculation using keywords 'energy' and 'element_energies'
  • add_connector - adds a connector dummy atom, see connector_type
  • set_connctor_dist - sets the distance of the connector from the anchor, see connector_distance
  • orient - align selected three atoms to origin, x axis and x-y plane
  • rotate_around_bond - rotates part of the system around bond defined by keyword 'bond_selection' by angle 'rot_angle'. The rotated part is the one containing the second atom in the bond selection.
  • rotate_xyz - rotate around origin in cartesian coordinates by angles specified by 'rot_angles_xyz'. Allows the use of keyword 'geometry_action_selection'.
  • randomize - modify coordinates randomly, with max. displacement defined by 'geometry_randomize_interval'
  • random_translation - shifts the geometry randomly with max. displacement defined by 'geometry_randomize_interval'
  • randomize_intermolecular - rotate molecules in a dimer randomly around all axes by angle +/-'rot_angle'. Afterwards, the intermolecular distance is adjusted so that the closest contact is at van der Waals distance.
  • symmetry - print the Schoenflies group if there is a symmetry within 'symmetry_tolerance'
  • symmetrize - symmetrize the geometry if there is a symmetry within 'symmetry_tolerance' (WARNING: The symmetrization tool may change the geometry slightly even if it is already symmetric!)
  • sort_mol_by_distance - sort individual molecules by distance from coordinate center
  • molden - visualize using Molden
  • get_info - print additional information stored in the geometry file
  • list_hbonds - print list of H-bonds
  • displacement_in_zmat - propagates a displacement (difference between geometry and geometry2) in z-matrix coordinates
  • series_energy_minimum - select the structure with the lowest energy (using energies available in the geometry file)
  • list_nc_hbonds - identify and list hydrogen bonds
  • update_charges - read atomic charges from a plain text file (keyword atomic_charges_read) and add them to the geometry
  • sum_charges - print a total charge obtained as a sum of atomic charges

geometry_action_selection: "%all()"

Some actions might work on specified selections, by default, all atoms are selected

geometry_action_selection_array: array

Keyword providing multiple selections to rmsd_fit_subset action

geometry_connect_break_symm: yes | no

Break the intermolecular symmetry by twisting the dimer around its axis and bending it out of axis sligtly.

geometry_connect_orientation: max_center_dist | min_center_dist

Handling of the intramolecular torsion coordinate (defined by molecule 1 center, connection axis and molecule 2 center). Value max_center_dist maximizes the distance of the center (trans- orientation), the other aligns the centers (cis).

geometry_connect_scan: array

Perform a distance scan in the connecting coordinate. Provide array of scaling factors to be applied to the intermolecular distance (by dafault, it is first set to vdW distance, for more options, see keyword geometry_connect_scan_ref_dist).

geometry_connect_scan_ref_dist: move_to_vdw | original

Reference distance (corresponding to scaling factor 1.0) for the scan.

  • move_to_vdw - before the scan, the intermolecular distance is set to vdW distance.
  • original - use original distance determined by the position of the connectors.

geometry_connector: "auto"

Connector selection for action connect. Applied to geometry. Value "auto" can be used to read the connector info from .xyz file comment line.

geometry_connector2: "auto"

Connector selection for action connect. Applied to geometry2. Value "auto" can be used to read the connector info from .xyz file comment line.

geometry_custom_vdw_radii: hash - a list of name: value pairs

Override vdW radii for some elements. Appliucable in geometry actions:

  • list_nc_closest_vdw and
  • connect_connectors

geometry_database_path: "."

Additional path searched for geometry databases. The default location, cuby4/data/geometries, is searched first and when the files are not found, this location is used.

geometry_load_charges: string

Atomic charges to be loaded into the geometry (reads the format produced by Cuby).

geometry_nc_shortest: yes | no

Used in the

geometry_nc_vdwlimit: 1.0

Distance limit (a scaling factor applied to vdw radii) used for selection of noncovalent interactions by the list_nc_... actions.

geometry_orientation: string

Three selections (semicolon-separated) defining orientation of the molecule. The molecule is moved so that the selected centers are aligned to the origin, x axis and x-y plane.

geometry_randomize_interval: 0.05

Max. random displacement (in Angstrom) applied to each coordinate by geometry actions randomize and random_translation.

geometry_reorder: original | reverse | random

Reordering of the input geometry.

geometry_rotate: string

If set, the geometry is rotated along the cartesian axes. Three angles (in degrees) should be provided, separated by commas. Use 'rand' for a random rotation.

geometry_setup_from_file: yes | no

Charge and multiplicity can be read from a remark in the geometry file. For now, only the .xyz format is supported where the second line should look like 'charge=X multiplicity=Y'. If this option is set and no data are found in the geometry, charge 0 and multiplicity 1 are assumed.

geometry_template: string

Template geometry into which the coordinates specified by the geometry keyword are loaded. This is an optional feature, when not set, the actual geometry is used directly.

geometry_update_coordinates: string

If set, the geometry read using the geometry keyword is updated with coordinates read from this file. This feature is useful e.g. to read coordinates into a PDB template for calculations that require the additional information from the PDB format.

geometry_update_zmat: hash - a list of name: value pairs

List of z-matrix coordinates updated after reading the geometry

geometry_write: ""

Name of a file to write the processed geometry to

geometry_write_append: yes | no

When set, geometry is added to the existing file

geometry_write_connectivity: original | from_radii | from_zmat

Some geometry formats (e.g. mol2) require writing the connectivity (list of bonds). By default, existing bond list is used or the connectivity is determined automatically from covalent radii. Optionally, rebuilding tghe connectivity canbe enforced or bonds from z-matrix can be used if the input file was z-matrix.

geometry_write_cuby_header: yes | no

Write header with information on the system cuby can work with (charge, multiplicity). Only some file formats support it (.xyz, .pdb, .mop) and the information must be present in the geometry. This overwrites any other header.

geometry_write_format: auto | xyz | pdb | mol2 | zmat | mop | cuby | sdf

Geometry file format of the output. By default, it is guessed from the file name. If the file name is /dev/stdout, the format of the input geometry is used if it is supported for writting.

geometry_zmat_bondlist: array

This keyword allows forcing the z-matrix builder to use selected bonds. The bond list is an array of atom selections defining the bonds - e.g. "1,2" or "3,5"

geometry_zmat_format: gaussian_vars | gaussian | mopac

Following z-matrix formats are availbale:

  • gaussian_vars - Gaussian format with named variables
  • gaussian - Gaussian format with inline values
  • mopac - format for MOPAC input

ghost_atoms: ""

Definition of ghost atoms (nucleus without a charge, basis set functions without electrons) by an selection expression. This is applied immediately after the geometry is loaded, before the 'selection' keyword is used to select some of the atoms.

gradient_cutoff: 10.0

Cutoff on gradient components, lower gradients set to zero

gradient_on_point_charges: yes | no

Calculate and print also the gradient on point charges. The gradient projection should be switched off.

gradient_projected: yes | no

Project out translation and rotation from the gradient. Nothe that this procedure is automatically carried out by some of the interfaces and external programs used to calculate the gradient.

h_bonds4_extra_scaling: hash - a list of name: value pairs

Manual definition of additional chrged sites to be scaled. Key of the hash is selection of donor/acceptor atoms to be applied to, value is a sacling factor.

h_bonds4_global_scaling: 1.0

Global scaling applied to the correction.

h_bonds4_parameters: hash - a list of name: value pairs

Parameters for the H-bond correction. By default, parameters for the selected method are loaded automatically.

h_bonds4_pt_corr: 0.0

Increase of proton transfer barriers

h_bonds4_scale_charged: yes | no

Scaling of the correction for charged groups (COO-, NH3+).

h_bonds4_skip_acceptor: array

Skip corerction for specific acceptor arrangement. Following cases are supported:

  • OS - oxygen bound to sulfur

h_bonds4_spx: yes | no

h_scan_energy_limit: 0.0

Accept only changes where the energy improves by more than this number

hessian_estimate: single_number | by_coordinate | from_lookup | fischer_almlof | lindh | swart | from_file | from_file_shift

Estimate of the initial hessian. It applies only to optimizations in redundant internal coordinates with quasi-Newton optimizers. The values are:

hessian_projected: yes | no

Project out translation and rotation from the Hessian. Nothe that this procedure is automatically carried out by some of the interfaces and external programs used to calculate the hessian.

hessian_read: ""

File name of the Hessian to be read (yaml format). If not specified or empty (default value), the Hessian is calculated.

hessian_write: "hessian.yaml"

File to write the calculated Hessian to. If the string is empty, Hessian is not written.

history_file: string

Name of the history file. If not specified, it is created from the name of the input file if possible, or is set to "".

history_freq: 1

History is written each history_freq steps. If set to 0, no history is written.

history_selection: string

If set, additional history file is written for a atoms selected by this keyword.

hof_energy_from_vibrations: yes | no

When set, the energy of the molecule is not calculated separtely but taken from the calculation of vibrations. To get a meaningful result, the setup in calculation_vib and calculation_ene must be identical because the latter is still used for calculation of atom energies.

ignore_recommendations: yes | no

Can be used to prevent the program exitting when a Recommendation is encountered. Recommendations are raised when cuby thinks the user attempts doing something wrong but technically possible.

init_hessian_lookup_file: string

File with a lookup table used for the construction of the estimate of the initial Hessian.

init_temp: 10.0

Temperature used to generate initial random velocities

interaction_check_size: yes | no

Check for atoms missing in selections of molecule_a and molecule_b.

interface: symbol

Interface used for the calulation. See the list of interfaces for possible values (online or by typing 'cuby4 interface' in shell). When the default value "auto" is used, cuby will attempt to choose the interface most suitable for the requested calculation method.

job: symbol

Job type (calculation protocol). The available protocols are listed in the documenation (page Protocols on the website, accessible from commandline by running 'cuby4 protocol').

job_cleanup: yes | no

Delete directories with external calculations when job finishes successfuly

job_title: string

Custom title for the job. When not set, protocol default is used.

lbfgs_n: 5

Number of vectors stored for l-BFGS

linesearch: none | quadratic_ls | old | cubic


  • none - only step scaling
  • quadratic_ls - quadratic function approximation with weighted least squares for its derivatives
  • old - quadratic function approximation with no respoect to values, only derivatives
  • cubic - cubic function approximation

maxcycles: 200

Maximum number of cycles of optimization or molecular dynamics

md_region: "%all()"

Selection of atoms moved in the simulation.

measurements: hash - a list of name: value pairs

A list of measuremens to be done, as a name: expression hash. For available measuremet expressions, see the documentation of the protocol 'measure'.

mem: 1000

Memory limit (in MB) passed to the external program if applicable. It should not be set to the full amount of memory available, allow some memory for the system. For parallel jobs, the amount of memory to be specified depends on the parallelization mode: For shared memory calculations, specify the total amount of memory, for MPI calculations, memory per core should be given.

mem_core: 25

Value in percent. Specifies how much memory is used for the user set "core", e.g. for integral storage, in QM calculations (Applies to Turbomole and ORCA).

mem_core_correlation: integer

Value in percent. Specifies how much memory is used for the user set "core" in corerlation energy calculation with RI. When not set, value of keyword 'mem_core' is used instead.

mem_core_scf: integer

Value in percent. Specifies how much memory is used for the user set "core" in RI-SCF calculation. When not set, value of keyword 'mem_core' is used instead.

mem_maxcor_max_scf: integer

Allows limiting the value of the maxcor input separately for SCF (in MB). Applied only when set, recommended value is 500.

merge_duplicate_calculations: yes | no

When enabled, the internal queue system of cuby identifies duplicate calculations and calculates them only once.

method: symbol

Computational method. This keyword must be specified when an external calulation is called using an interface that implements more methods. If the interface implements only one method, it is used by default. The list of available methods can be found in the documentation, either online or by command 'cuby4 method'. For example, common methods are HF, MP2, CCSD(T), forcefield, AM1...

mixer_weight_a: float

Weight for calculation a. The calculation should be defined in a block calculation_a.

mixer_weight_a_expression: string

Weight for calculation a evaluated as ruby expression. Overrides the numeric value provided in mixer_weight_a.

mixer_weight_b: float

Weight for calculation a. The calculation should be defined in a block calculation_a.

mixer_weight_b_expression: string

Weight for calculation a evaluated as ruby expression. Overrides the numeric value provided in mixer_weight_b.

mndo_exe: ""

Path to the mndo executable.

modifiers: list of symbols

A list of interfaces applied as a modifiers to this calculations. Setup for each modifier should be provided in a block modifier_modifiername.

molpro_exe: ""

Path to the molpro binary

molpro_key: ""

Molpro license key. It has to be set only when Molpro can not find the key it was installed with.

molpro_ld_path: ""

Path to libraries used by molpro (such as MKL).

molpro_lib_dir: ""

Path to the directory containingi basis set libraries etc. needed by Molpro (set using the -L commandline option).

molpro_mpirun: ""

Path to mpirun used to run Molpro in MPI mode.

molpro_sapt_df_level: 3

Level of density fitting in DFT-SAPT. Values from 0 (no DF) to 3 (most approximate).

mopac_corrections: none | d2 | h2 | dh2 | dh+ | d3 | h4 | d3h4 | d3(h4) | d3h4x | org

Corrections for noncovalent interactions for PM6 as implemented in MOPAC.

mopac_cosmo2_scale_missing_radii: 0.0

Defines how the atomic radii for element not included in the original parametrization are treated. When set to 0 (default), the original value provided by MOPAC is used. When set to other value, the radius is calculated by scaling the vdW radius by this number.

mopac_cosmo2_surf_tension: float

Surface tension parameter in the COSMO2 solvation model (in kcal/mol/A^2). A method-specific default value is used when the keyword is not set.

mopac_cosmo_nspa: integer

mopac_cosmo_radii: hash - a list of name: value pairs

Van der Waals radii for COSMO. Hash element: radius.

mopac_damp_scf: float

SCF convergence damping. Passed to the DAMP keyword.

mopac_exe: ""

MOPAC executable

mopac_external_params: hash - a list of name: value pairs

Allows modification of the semiempirical parameters from cuby input. When set, the keyword EXTERNAL is added to the input automatically.

mopac_keywords: ""

Extra keywords (in the MOPAC format) added into the input

mopac_mozyme: yes | no

Use of the linear scaling MOZYME algorithm. MOPAC documentation:

mopac_parallel: yes | no

The latest version allows parralelization, but the input can not be used with older versions of MOPAC2012. Disable this option when older version is used.

mopac_peptide_bond_fix: yes | no

Controls the corerction for peptide bond torsion. It was introduced as an addition to the RM1, PM6 and PM7 methods, therefore it is switched off by default for backwards compatibility. MOPAC documentation:

mopac_precise: yes | no

Use tight thresholds, needed for accurate gradient. MOPAC documentation:

mopac_relscf: float

Relative accuracy of SCF calculation (multiplier for convergence thresholds) passed to RELSCF keyword.

mopac_setcharge: hash - a list of name: value pairs

Manual specification atomic charges for MOZYME, hash of charges indexed by atom selection. The charge can be '0', '+' or '-'. Described at

mopac_setpi: array

Manual specification of double bonds for MOZYME, array of atom pairs (defined by two selection expressions separated by semicolon). MOPAC documentation:

mopac_setpi_silent: yes | no

Disables printing of information on setpi matching patterns.

mopac_version: mopac2012 | mopac7

Version of MOPAC to be used. By default, MOPAC 2012 (and above) is used, it is however possible to switch to the legacy MOPAC 7 but the functionality is limited.

mrcc_bin_dir: ""

Path to the directory with mrcc executables

mrcc_extra_keywords: ""

Custom keywords inserted into the mrcc input

mrcc_parallel_ccthreads: 1

No. of threads in coupled clusters parallelization.

mrcc_parallel_mpi: 1

No. of MPI tasks in the combined MPI/OMP parallelization.

mrcc_restart_cc: yes | no

Attempt restarting coupled clusters, skipping SCF step. Restart and integral files from a previous run must be present.

multiplicity: 1

Spin multiplicity - required for all QM calculations. If not set, a default value 1 is used silently.

multistep_print: yes | no

Controls printing of step headers and output of each step

multistep_result_eval: string

Alternatively to multistep_result_expression, a piece of ruby code can be called on the results. For experts only.

multistep_result_expression: string

The result of a multistep job is evauated using this expression after all the steps have been completed. For experts only, this requires calling internal data structures of the multistep job.

multistep_result_name: "Result expression value"

Name of the result calculated using multistep_result_expression keyword

neb_fconst: 20.0

Force constant of the harmonic potential connecting the points on the elastic band (kcal/mol/A).

neb_mep_file: ""

The file to which the minimum energy path is written to. It is updated in each step.

neb_mep_file_archive: yes | no

Archive minimum energy path in each step, file names are based on keyword neb_mep_file. The file to which the minimum energy path is written to. It is updated in each step.

neb_optimize_endpoints: yes | no

Optimization of the end points of the MEP can be disabled if the provided geometries are already optimized.

neb_version: improved | original

Version of the formulation of the NEB, see the references in the documentation.

numerical_gradient_atomic_charges: yes | no

Optional calculation of the derivatives of the atomic charges.

numerical_gradient_step: 0.0025

numerical_gradient_type: single_sided | central | tetrahedral

Number of points per atom used for numerical differentiation:

  • single_sided - 3 points, least robust
  • central - 6 points, most accurate
  • tetrahedral - 4 points

numerical_hessian_e_order: 2

Hessian from energy: Order of the formula (2 or 4)

numerical_hessian_step: 0.001

The size of the displacemeni (in Angstrom) used in the numerical differentiation.

numerical_hessian_type: single_sided | central | tetrahedral | energy_only

Number of points per atom used for numerical differentiation:

  • single_sided - 3 points, least robust
  • central - 6 points, most accurate
  • tetrahedral - 4 points
  • energy_only - parabolic fit from energies (the other methods use gradient)

opt_auto_restart: yes | no

When enabled, restart file '' is written in each step, and if this file is found at the beginning of an optimization, the geometry is updated with coordinates from this file.

opt_convlimit_e: 0.006

Convergence limit for energy change between steps (kcal/mol). If set to 0, this criterium is not evaluated.

opt_convlimit_max_g: 1.2

Convergence limit for maximum gradient component (kcal/mol/A). If set to 0, this criterium is not evaluated.

opt_convlimit_rms_g: 0.6

Convergence limit for root mean square of gradient (gradient norm) (kcal/mol/A). If set to 0, this criterium is not evaluated.

opt_diagonal_h0: 1000

Initial value of diagonal elements of the hessian

opt_freeze_cartesian: hash - a list of name: value pairs

Allows freezing some cartesian coordinates. The input should be a hash in a form "atom_index: xyz" (only some coordinates can be selected, e.g. by "x" or "xz")

opt_qn_update_formula: bfgs | dfp | broyden | sr1 | dfp_bfgs | sr1_bfgs

Hessian update formula for quasi-Newton optimizers

opt_quality: 1.0

One-number control of optimization quality - multiplier of convergence limits. The default value sets rather loose thresholds suitable for optimization of rigid molecules only. When accurate geometries of flexible molecules or noncovalent complexes are needed, opt_quality should be set to 0.1 or lower.

opt_refuse_steps: yes | no

Refuse bad optimization steps and try shorter one

opt_tr_mode: abs | max | components

Step size scaling mode for RFO, QN and LBFGS (TRIM uses another means of step size control):

  • abs - Step is scaled so that its absolute value is not larger than the limit
  • components - Each component of the step vector is scaled separately
  • max - Step is scaled so that the largest component is not larger than the limit

opt_tr_update: yes | no

Update of trust radius during the optimization

optimize_print: steps | steps_as_dots | final_energy | statistics (list, more items can be selected)

Optional printing:

  • steps - print complete information in each step
  • steps_as_dots - one character per step, dot or 'o' and 'O' as more criteria are fulfilled
  • final_energy - print final energy after optimization
  • statistics - print counts of various events encountered by the optimizer

optimize_region: "%all()"

Selection of atoms to be optimized.

optimize_ts: none | lowest_eigenvector

Optimization to transition state. Available only in optimization using Hessian calculated in each step.

optimizer: auto | rfo | trim | trim_hessian | lbfgs | plbfgs | quasi_newton | nelder_mead | genetic

Optimization algorithm. The default option 'auto' switches between quasi-Newton (BFGS) for small (less than 100 atoms) and LBFGS optimizers. The 'trim_hessian' uses the TRIM (trust radius image minimization) algorithm with Hessian calculated in each step. The Nelder-Mead simplex method and genetic algorithm are not intended for geometry optimization but for other applications.

orca_bin_dir: ""

Path to the directory containing the orca binaries

orca_dispersion_correction: none | d3bj | d3zero | nl | scnl | d4

Dispersion corrections calculated in Orca.

orca_dlpno: yes | no

Enable the Domain-localized pair natural orbitals approximation in CCSD and CCSD(T) calculation.

orca_dlpno_accuracy: tight | normal | loose | custom

DLPNO thresholds (loose/normal/tight). If the value "custom" is used, the thresholds can be manually defined using orca_extra_input keyword.

orca_ecp: none | auto

Pseudopotentials. When set to 'auto', ORCA assigns pseudopotentials automatically fot the selected basis sets.

orca_ecp_file: string

File with custom ECPs passed to the basis block

orca_extra_input: ""

orca_guess: hcore | hueckel | patom | pmodel

Guess for starting SCF. When not set, Orca's default is used

orca_keywords: ""

Additional keywords passed to ORCA, in the simple format (a line beginning with !)

orca_mpi_setup: ""

A shell command(s) for loading the MPI environment (parallel-calculations only)

orca_opt_coords: redundant | cartesian

Orca native optimization coordinate system

orca_optlimit_d: 0.0001

Orca native optimization convergence limit in terms of step size (max and rms) (a.u.)

orca_optlimit_e: 1.0e-06

Orca native optimization convergence limit in terms of energy change (a.u.)

orca_optlimit_g: 1.0e-05

Orca native optimization convergence limit in terms of gradient (max and RMS) (a.u.)

orca_rijcosx: yes | no

Use the RIJCOSX (RI-J chain of spheres) approximation for HF exchange calculation.

orca_smd_free_energy: yes | no

Add a standard state correction term (just a constant) to make the SMD output comparable with experimental solvation free energies - see Orca manual on SMD.

orca_version: "3.0.0"

Version of ORCA. This keyword has default value '3.0.0' for backwards compatibility, do not forget to set it to proper number if using newer version of ORCA.

parallel: 1

Number of CPUs used by the external program running in parallel mode.

parallel_mode: default | mpi | shm | omp

Mode of parallel execution of the external software. Use the value 'default' unless the external program supports multiple options. The options are:

  • MPI - message passing interface (note that each CPU uses the memory provided by mem keyword)
  • SHM - general shared memory
  • OMP - OpenMP, shared memory multi-threaded mode

param_exe: ""

PARAM executable

param_inputs_dir: string

Directory with the .mop files

param_method: string

Method to be parametrized, such as PM6

pdb_extra_columns: yes | no

Controls printing of additional columns in PDB files (beyond coordinates). Applicable to all tasks where PDB file is written.

pdb_rename_residues: hash - a list of name: value pairs

Renaming of PDB residues. Hash in form atom_selection: new_name.

pdb_resno_start: 1

Number of first PDB residue for pdb_renumber

pdb_set_chain: "X"

PDB chain value for action pdb_selection_as_chain

periodic: yes | no

Switches on periodic boundary conditions. Note that this is supported by only very few interfaces.

periodic_box: array

Periodic box specification. Cuby now supports only rectangular boxes. If one number is provided, a cubic box is used. Three numbers can be provided to set the box dimensions in x, y and z axis. At present, the box has to be specified in the input, cuby does not read if from the geometry.

periodic_box_origin: array

The origin of the periodic box in the cartesian coordinates can be set by this keyword. The default is the origin ([0,0,0]).

plbfgs_colors: 1

How many colors to to calculate in one step. The number of calculations is then 1 + 3 * plbfgs_colors. The most efficient setup is to keep the number of colors 1 and set cuby_threads to 4 to perform all the four calculations in parallel.

plbfgs_init_d: 1.0e-05

init. value of d for num. differentiation

point_charges: ""

A list of point charges defining an extarnal electrostatic field. One charge per line, in format x y z charge. (Coordinates in Angstrom, charge in elemental charge units). Note that only some interfaces support the use of point charges.

position_difference_threshold: 0.1

Threshold for differences between atom positios (in Angstroms)

prepare_only: yes | no

When enabled, cuby prepares the calculations and exits before running them.

print: timing | energy_decomposition | subsystem_results | dipole | polarizability | input_geometry | step_timing | gradient | molecular_orbitals | homo_lumo (list, more items can be selected)

List of extra features to be printed:

  • timing: print time spent in the program (global)
  • energy_decomposition: components of the calculated energy, if they are present (global)
  • subsystem_results: print results for subsystems (protocol interaction, threebody)
  • dipole: dipole moment, if available
  • polarizability: molecular polarizability, if available
  • input_geometry: print the geometry used at the beginning of the calculation (global)
  • step_timing: print timing for individual steps of the calculation (protocol optimize)
  • gradient: print gradient used in the optimization (protocol parametrize)
  • molecular_orbitals: print all molecular orbitals
  • homo_lumo: print energies of frontier orbitals

properties: static_polarizability (list, more items can be selected)

Calculation of additional properties

pseudopotentials: string

Pseudopotential to be applied to all atoms. None used when not set.

pseudopotentials_elements: hash - a list of name: value pairs

Specification of pseudopotentials for selected elements. The format is a hash element: "pseudopotential_name"

psi4_bin_dir: ""

Path to the directory containing the psi4 binaries

psi4_data_dir: ""

Path to the psi4 data directory

psi4_df_guess: yes | no

Use density fitting calculation as a guess for a regular SCF.

psi4_fno: yes | no

Frozen Natural Orbitals approximation in MP3, CCSD and CCSD(T) calculations.

psi4_geometry_fragments: yes | no

Separate fragments in DFT geometry. Two fragments should be defined in blocks molecule_a and molecule_b. Keywords charge, multiplicity and selection are needed.

psi4_keywords: ""

Additional keywords to be added to the Psi4 input.

psi4_python_version: 2

Version of the python used by psi4 (2 or 3)

psi4_restart_on_segfault: yes | no

We have encountered some random crashes during the initialization of the calculation. With this keyword set to on (default), cuby attempts to restart the calculation several times before it reports an error.

psi4_sapt_ct: yes | no

Switch on additional SAPT calculations to separating charge transfer energy as a difference between SAPT polarization in monomer and dimer basis.

psi4_sapt_level: sapt0 | sapt2 | sapt2+ | sapt2+(3) | sapt2+3

psi4_version: "1.0"

Version of the psi4 package, with one decimal - e.g. "1.0".

qmmm_add_ter: ""

Selection of atoms in QM regieon (selection expression) after which PDB TER labels are added.

qmmm_charges_around_links: 0

Removal of embedding charges around link atoms. The value is a number of bonds defining the distance. Zero means only the charge on the atom replaced by a link atom is removed, value of 1 selects also atoms boud to it etc.

qmmm_charges_extra_info: yes | no

Store information on the original atom in the point charges. Not needed unless a specialized calculation with a QM interface that supports this is used.

qmmm_core: string

Selection of QM core in QM/MM calculation

qmmm_cut_bonds: array

List of bonds that are cut and replaced by link atoms

qmmm_embedding: mechanical | electrostatic_2way | electrostatic

The "embedding" used:

  • mechanical - all the intraction between the QM region and the rest of the system is treated by MM
  • electrostatic_2way - the interaction of the QM region with the point charges modeling the rest of the system is included in the QM Hamiltonian
  • electrostatic - the same as above but with inexact gradient (energy is the same)

qmmm_geometry_only: yes | no

If set, the program is aborted after preparation of the QM region but before the calculations are prepared.

qmmm_qmregion_file: "qm_region.pdb"

Name of the file to which geometry is written to. Set to empty string to prevent writting this file.

qmmm_remove_charges: ""

Selection of MM atoms not to be used as point charges in electrostatic embedding. By default, charges are removed from the atoms in the bonds across QM/MM boundary, this option can only add to this.

qmmm_rename_residues: array

List of residues to be renamed in QM region. Format: YAML array of strings "selection new_name".

qmmm_wat_center: string

Selection of atoms defining the center of the solvent sphere

qmmm_wat_k: 5.0

Force constant for attraction of the QM water, in kcal/mol/A^2

qmmm_wat_num: float

Number of waters in the QMMM regions (waters clostest to the center defined by qmmm_wat_center are selected)

queue_extra_commands: ""

Additional comands to be inserted into the shell script that executes cuby on the node - useful for e.g. seting up the environment.

queue_force_resubmit: yes | no

Submit job anew even if it looks like it was already submitted.

queue_jobname: "cuby4"

Name of the job passed to the queue system.

queue_mem_per_cpu: string

Memory per CPU, in any units recognized by the queue system

queue_mpiprocs: integer

Number of MPI processes per node. Needed only for MPI jobs.

queue_name: "N/A"

Name of the queue to be used.

queue_nodes: 1

Number of nodes to be allocated. Note that parallelization across nodes is not supported by most cuby interfaces.

queue_ompthreads: integer

Number of OMP threads per process. Needed only for some jobs.

queue_output_file: "LOG"

Name of the file to which output of cuby is redirected.

queue_parallel: integer

Number of CPUs allocated in the queue system (per node). If not set, it is calculated from other keywords as parallel * cuby_threads

queue_qsub_command: "qsub"

The command for submitting the jobs to queue.

queue_qsub_options: ""

Additional commandline options for the command submitting the job (usually named qsub).

queue_results_dir: "RESULTS"

Directory where the results are put to after job finishes. Path is relative to the directory in which the job is submitted.

queue_scratch_dir: "N/A"

Directory where the calculation is run on the node. Evaluated in a bash script, can contain environment variables. A subdirectory with unique name is created for each job in the scratch directory.

queue_slurm_cpus_per_task: 1

Passes "--cpus-per-task" option to SLURM

queue_slurm_exclusive: yes | no

Passes "--exclusive" option to SLURM

queue_slurm_ntasks: 1

Passes "--ntasks" option to SLURM Passes "--cpus-per-task" option to SLURM

queue_submit: yes | no

Submit the job to queue instead of running it immediately. The submission system must be configured accordingly.

queue_system: run_in_background | pbs | sge | slurm | lsf

Queue system used:

  • run_in_background - example only, runs the cuby job in background immediately.
  • pbs - use the PBS queue system
  • sge - use Sun Grid engine
  • slurm - use the Slurm Workload Manager
  • lsf - IBM LSF scheduler

queue_wait_until_finished: yes | no

Keep waiting while the job is queued and running.

queue_walltime_hrs: 24

Requested walltime passed to the queue system.

random_seed: integer

Random seed used to initialize the random number generator when setting up a MD run. When not set, random initialization is used.

reaction_formula: string

Reaction formula, in format e.g "2A + B -> C + 2D"

reaction_geometries: hash - a list of name: value pairs

List of geometries of all molecules, in the order they are presented in the formula

reaction_print: formula (list, more items can be selected)

Controls the output of the protocol. Allowed options are:

  • formula - print the reaction formula (on by default)

reaction_smiles: yes | no

Generate the geometries of the molecules using SMILES notation from the formula itself

redcoord_all_torsions: yes | no

Generation of redundant coordinates - use all torsions

redcoord_extra_contacts: yes | no

Add extra contacts to the redundant coordinates

redcoord_freeze_class: bonds | angles | torsions (list, more items can be selected)

Freeze some class of internal coordinates

reduce_core_element: hash - a list of name: value pairs

Allows to reduce frozen shells per element, for use with pseudopotentials.

remote_calculations: no | drb

Mode of parallel (specified by -->cuby_threads) remote execution of calcualtions. The options are:

  • no - calculations are run locally in multiple threads
  • drb - calculations are run at remote servers using drb (distributed ruby), URIs of the servers must be provided in -->remote_drb_servers

remote_drb_servers: array

List of URIs of the remote servers (the URI is printed when the server is started)

remote_file_transfer: shared_wd | scp

Specifies how the calculation files are transferred to a node:

  • shared_wd - no transfer, all calculations use a shared storage
  • scp - files are copied using ssh

remote_servers_close: yes | no

Shut down remote servers when the calculation is finished

remove_rotation: yes | no

Removes rotational component of a gradient in each cycle of optimization or MD a velocity in MD simulation.

remove_translation: yes | no

Removes translational component of a gradient in each cycle of optimization or a velocity in MD simulation.

replace_energy_with_component: symbol

Replace the total energy in the result with a selcted component of it. The original energy is stored in a component "original_energy".

replace_energy_with_eval: string

Replace the total energy with a result of a ruby eval call - the result can be constructed from any other varibles.

replace_energy_with_expression: string

Replace the total energy in the result with an arbitrary expression using the energy components. The original energy is stored in a component "original_energy".

restart_file: string

Name of file to which the last geometry is written. When not specified, the name of the file is "" if the job is an optimization and it has converged, and "" if it did not. For MD, the default is also "". Setting the value to "" means no restart file is written.

restart_file_append: yes | no

By default, the restart file is overwritten, use this option to append the coordinates to an existing file

restart_file_converged: string

Name of file to which the last geometry is written if the optimization converged. When not set, the behaviori is specified by 'restart_file' keyword.

restraint_cp_fc: float

Force constant of the restraining potential, in kcal/mol/A^2.

restraint_cp_flat_r: 0.0

Radius of the flat bottom of the potential.

restraint_cp_selection: "%all()"

Selection of atoms the restraints are applied to. By default, all atoms in the geometry are selected.

restraints: array

List of restraints. Each line has format: distance|angle|torsion|distance_difference; value; force_constant; atom_selection1; atom_selection2; ... Angles are specified in degrees

rot_angle: float

Angle (in degrees) for rotation operations.

rot_angles_xyz: string

Three angles (in degrees) for rotation in cartesian space, as three comma-separated values

ruby_commands: string

Commands to be executed using ruby's eval

s6: 1.0

Scaling of the dispersion energy

scan_generator: none | grid_xyz | z-matrix | interpolate_zm

By default, the scan is performed on a series of geometries provided by the user. The scan generator can be used to generate this series on the fly.

scan_generator_batchsize: 0

When set to 0 (default), a series of geometries is saved in a single file and immediately calculated. If set to nonzero number, the scan is divided into batches of this size which are saved in separate directories so that they can be run independently.

scan_generator_setup: hash - a list of name: value pairs

Setup for the scan generator. Different options are available for different generators, see the protocol documentation.

scan_mode: serial | parallel

In the default (parallel) mode, all calculations of teh scan are prepared and then run using the internal queue system of cuby, which can run multiple calculations in parallel. In the serial mode, only one calculation is set up and repeatedly called with the changing geometries.

scan_print_mode: numbers | simple | full

Mode of printing scan results:

  • numbers - just a column(s) of numbers are printed
  • simple - one result per line, with some description
  • full - Verbose output from the child protocol. Only this option is available for all protocols.

scf_convergence: 7

SCF convergence threshold (energy), set to 10^-X a.u.

scf_cycles: 50

Maximum number of SCF iterations

scf_integral_storage: default | disc | direct | mixed

Integral storage in SCF. When not set, the default option of the interfaced program is used. The other options are:

  • disc - store everything on disc
  • direct - recalculate on the fly
  • mixed - optin specific to deMon interface

scf_levelshift: float

Shift of virtual orbitals (in a.u.). When the keyword is not set, default value of the external program is used.

scf_multipole_expansion: yes | no

Multipole expansion in evaluation of coulomb integrals.

scs_os: 1.2

SCS scaling for "opposite spin" term. The default value is for SCS-MP2.

scs_ss: 0.333333

SCS scaling for "same spin" term. The default value is for SCS-MP2.

selection: "auto"

Atom selection using cuby's selection language. The default value is context-dependent:

  • At the root level, where the selection defines what part of the geometry is loaded, the default is %all(), loading everything
  • In selection of a subsystem (e.g. for interaction energy calculation), first molecule becomes the first subsystem etc...

serial_scf: yes | no

Run SCF part of calculation in serial and paralellize only the correlation part.

shell_commands: string

Commands to be executed in the default shell (using the system call from ruby).

shell_script_after_calculation: string

  • Execute shell commands after a calculation is run

shell_script_after_prepare: string

  • Execute shell commands after a calculation is prepared but before it is run

shell_script_before_calculation: string

  • Execute shell commands before a calculation is run

skip_devel_warnings: yes | no

Disables warnings on devlopment status of interfaces.

skip_step_if_eval: string

Condition allowing skipping a step based on evaluating a ruby expression in the current context. The results of the previous step are available in variable 'previous_step.results'.

skip_step_if_file_found: string

Condition allowing skipping a step if some file already exists

skip_step_if_file_not_found: string

Condition allowing skipping a step if some file is missing

smiles_engine: balloon | obabel

External tool for building 3D geometries from SMILES.

solvent_epsilon: 78.5

Dielectric constant of implicit solvent

solvent_model: symbol

Implicit solvent model. Different interfaces support various solvent models (if any), see the documentation of the interface. The properties of the solvent are defined by the keywords "solvent_epsilon" or "solvent_name" (depending on the interface)

solvent_name: "water"

In some programs, the solvent is specified by its name - see the respective documentation.

sos_scaling: yes | no

SOS (scaled oppposite spin) scaling in MP2. No further input needed, scaling of 1.3 is used. Nn contrast to full SCS, the second component is not calculaed at all. Ref: J. Chem. Phys. 121, 9793 (2004);

sos_scaling_laplace: 0

When set to nonzero value, accelerated Laplace-transformed SOS-MP2 is used. The value of the keyword specifies the threshold (10^-X a.u.) used (4 or 5 is recommended).

spin_component_scaling: yes | no

SCS scaling in MP2. Use scs_ss and scs_ss keywords to set the scaling coefficients.

spin_restricted: rhf | uhf | auto_uhf

Restricted/Unrestricted spin treatment. The value 'auto_uhf' swiches on UHF for any open-shell system while RHF is used for closed shells.

sr: float

Radii scaling for damping function

start_from_previous: yes | no

Use results from previous step (of, e.g. geometry optimization) as a starting point for the calculation

step_queue: yes | no

When set in a step block, the calculation is queued until a following steps triggers execution of the queue

step_title: string

Custom step title, step name is used if not set

step_title_decoration: "="

Character using in the decoration lines in step titles

steps: list of symbols

List (comma separated, or YAML array) of the names of the steps. Each step is then defined in a subsection named "calculation_stepname". Common setup shared by all the steps can be defined in subsection "calculation_common", this setup can be overriden by the setup of a particular step.

store_geo_in_results: yes | no

Add also the geometry to the results object - useful when combined with 'write_results_yaml'

symmetry_tolerance: 0.01

Tolerance for determination of symmetry (as RMSD in Angstrom)

symmol_exe: ""

Path to external program symmol ( used for symmetry determination / symmetrization.

temperature: 300.0

Temperature to be maintained by the thermostat

temperature_target: float

When set, the thermostated temperature is varied during the simulation, starting with the one set by keyword temperature and linearly interpolating to this value at the end of simulation.

template_mopac_exe: ""

MOPAC executable to be used

test_name: ""

Name of the test printed in the report

test_print_results: yes | no

Print the original results in addition to the test report

test_result: string

The result the tested calculation should yield. The value is converted to and tested as quantity defined by keyword test_result_type.

test_result_type: energy | gradient | dataset

Type of the result tested:

  • energy - energy is compared
  • gradient - absolute value of the gradient is compared
  • dataset - RMSE over the dataset is compared

test_threshold: 0.0001

The threshold defining a successful test.

thermo_low_mode_fix: none | as_rotations | as_rotations_including_negative

Special treatment of low frequency modes in thermodynamics calculations:

  • none - no fix applied
  • as_rotations - Low mode entropy correction by Grimme[DOI: 10.1002/chem.201200497]
  • as_rotations_including_negative - same as above, including negative frequencies

thermo_pressure: 101325.0

Pressure for the thermodynamics calculations, in Pa. The default is 1 atm.

thermo_symmetry_number: 1.0

Symmetry number for the thermodynamics calculations.

thermo_temperature: 298.15

Temperature for the thermodynamics calculations, in K.

thermostat: none | berendsen | andersen | nose-hoover | bussi

Selection of thermostat algorithm

thermostat_tc: 0.5

Thermostat time constant (ps) setting strength of the coupling to the thermostat. The exact mening of the value is different in different algorithms.

timestep: 0.001

Timestep for MD (ps)

tm_parallel_mode_defaults: hash - a list of name: value pairs

A lookup for parallel_mode == default which allows specifying paralellization mode (mpi, shm, omp) for individual turbomole modules.

torchmd_model: ""

File with the model (.ckpt)

torchmd_multiplier: 1.0

trajectory_file: string

Name of the file the trajectory is written to. By default, it is "trajectory" + base name of the input file + a suffix for the selected file format.

trajectory_format: xyz_velo | xyz

Format of the trajectory:

  • xyz_velo - .xyz file with extra columns for velocities in Angstrom/ps units
  • xyz - plain .xyz format, velocities are not written

trajectory_freq: 1

Frequency of writing the trajectory (every Nth step). If set to 0, no trajectory is written.

trajectory_selection: "%all()"

Selection of atoms written to the trajectory. By default, trajectory of the whole system is logged. Optionally, only selected atoms (specifed using the cuby selection expression) could be saved. A special value "md_region" makes this selection equal to the selection of the moving region (see md_region keyword).

trust_radius: 0.1

Trust radius (max. step size) in Angstrom.

trust_radius_max: 0.3

Upper limit of trust_radius when dynamic change of it is allowed (by opt_tr_update)

trust_radius_min: 1.0e-07

Lower limit of trust_radius when dynamic change of it is allowed (by opt_tr_update)

turbomole_bin_dir: "N/A"

Path to the turbomole bin directory (serial version)

turbomole_ccsd_cycles: integer

Sets maximum number of CCSD iterations. When not set, turbomole uses its default value.

turbomole_cosmotherm_dir: "N/A"

Path to the cosmotherm installation

turbomole_esp_grid: string

When set, electrostatic potential calculation is requested on a grid defined in file referenced by this keyword. The grid is defined as x y z coordinates in Angstrom.

turbomole_keywords: ""

Extra keywords to be added to the turbomole control file.

turbomole_save_system_info: yes | no

Save system information (disk space, etc...) before each call of a turbomole binary

turbomole_scf_grad: yes | no

Calculate and save a separate SCF gradient before post-HF gradient is calculated.

turbomole_scf_ri_jk: yes | no

Apply the RI approximation also to Coulomb integrals (RI-JK) method, instead of just exchange (RI-J).

turbomole_scf_ri_marij: yes | no

Multipole-accelerated resolution of identity approximation for HF/DFT calculation. Turbomole's default setup is used.

turbomole_skip_scf: yes | no

Skip the SCF step. This allows running additional correlation calculation on an independently performed SCF calculation.

turbomole_turbodir: "N/A"

Path to the base of turbomole installation

turbomole_version: N/A

Version of turbomole used

turbomole_weight_derivatives: yes | no

Enable more accurate gradient calculations in DFT.

use_symmetry: yes | no

Allow the use of symmetry in the QM calculation

velocities: random | zero | read

Assignment of initial velocities. The options are:

  • random - random velocities from a Gaussian distribution coresponding to the temperature set by init_temp keyword
  • zero - simulation starts with zero velocities
  • read - read velocities from a file specified by the velocities_file keyword

velocities_file: string

verbosity: silent | minimal | brief | normal | debug

Verbosity of the output:

  • silent - nothing is printed
  • minimal - just the most important results are printed in format intended for machine reading
  • brief - just the most important results are printed in human readable form
  • normal - all necessary iinformation is printed with 'decorations'
  • debug - same as normal + debugging messages

void_delay: 0.0

Time (in seconds) spent in the void "calculation"

void_energy: 0.0

The energy returned by the void interface (zero by default)

waterball_center: solute | origin | fixed_solute

Center of the waterball:

  • solute - waterball defined relative to the solute center of mass
  • origin - 0,0,0 coordinate
  • fixed_solute - 0,0,0 coordinate for waterball, the solute center of mass is connected to it by a harmonic restraint

waterball_solute: string

Selection defining the solute or the center of solvation in it. Required when waterball_center is set to solute or fixed_solute

waterball_solute_k: 5.0

Force constant of the restraint holding the solute close to the origin of the coordinate system, applies only to waterball_center = fixed_solute

write_parsed_input: yes | no

If enabled, the parsed input, including all modifications by cuby (e.g. child calculation setup and defaults used) is saved to file "parsed_input.yaml".

write_results_yaml: string

Write serialized results in YAML format to this file.

x0: float

A generic parameter used in development

x1: float

A generic parameter used in development

x2: float

A generic parameter used in development

x3: float

A generic parameter used in development

x4: float

A generic parameter used in development

x5: float

A generic parameter used in development

x6: float

A generic parameter used in development

x7: float

A generic parameter used in development

x8: float

A generic parameter used in development

x9: float

A generic parameter used in development

xbond_only_noncovalent: yes | no

When set, covalent bonds and 1-3 and 1-4 covament neigbors are excluded from the corrected pairs.

xbond_parameters: hash - a list of name: value pairs

Two-level hash, indexed by 1) halogen element and 2) acceptor element, the value should be array of the k and e parameters. The parameters defined here are merged with the default parameters for D3H4X correction.

xtb_home_dir: ""

XTB home directory (should contain parameter files and binary in 'bin' subdirecory).

xtb_options: ""

Additional commandline options for the xtb code

zmat_displace_amount: float

The magnitude of the displacement in the z-matrix coordinates for action displacement_in_zmat. The value has undefined dimension, the actual displacement depends on the nature of the coordinate. Try values in the range of units or tens.

zmat_displace_coords: distance | angle | torsion | distance_im | angle_im | torsion_im (list, more items can be selected)

Selection of the coordinates displaced using displacement_in_zmat. The *_im options apply only to intermolecular coordinates.