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Nonpolar (surface-area dependent) energy for generalized Born solvent model. By default, none is used. Available options are:
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.)
Additional commands passed to leap, executed after the system is loaded but before the topology is saved.
Automatically add dislulfide bridge bonds between nearby CYX residues.
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):
Cuttoff for non-bonded interaction. The default value is very large so that all interactions are evaluated.
Convergence limit for OpenMM optimization (max. element of gradient)
List of coordinate/angle restraints, in format similar to the one used in the restraints interface
Convergence limit for geometry optimization in AMBER. Evaluated as root-mean-square of the Cartesian elements of the gradient, in kcal/mol/A.
Nonpolar energy for Poisson-Boltzman model. By default, none is used. Available options are:
Configuration: path to sander executable. By default, it is taken from AMBERHOME directory, but this can be overriden manually.
When specified, user-provided topology file is used, otherwise cuby calls leap to generate it
Set force constants for dihedrals to zero. This is achieved by modification of the topology file.
Energy correction (in kcal/mol) applied to each atom of given element.
Method of atomic charges calculation:
Cap charges on selected elements at maximum/minimum value. The excess charge is redistributed according to keyword atomic_charges_cap_redistribute.
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).
Name of the file to write the atomic charges to. If not set, the charges are only printed but not saved to a file.
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 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.
Specification of other auxiliary basis set for selected elements. The format is a hash element: "basis_name"
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.
Specification of other auxiliary basis set for selected elements. The format is a hash element: "basis_name"
Specification of other basis set for selected elements. The format is a hash element: "basis_name"
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:
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.
Selection of one bond in the system, provided as two atom selection separated by semicolon.
Counterpoise correction:
Definition of the cDFT constraints, Array (each item defines one constraint) of Hashes with following opions:
Enables electron transfer coupling in cDFT calculations, two constraints with flags 'donor' and 'acceptor set to true must be present
Path to libraries used by CFOUR, added to LD_LIBRARY_PATH before the program is executed.
Molecular charge - required for all QM calculations. If not set, a default value 0 is used but a warnig is printed.
Calculate monomer charges from atomic charges (the geometry must be read from a file containing atomic charges)
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.
When using "charge_from_file", this value can be added to the charge read from the file.
Charge-dependent PB solvation model - parameter A for each element
Charge-dependent PB solvation model - parameter B for each element
Path to the parallel charmm executable (or a script that sets up the MPI environment and then runs charmm)
Extra options for charmm, included directly into the input file before the actual calculation.
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
Array of paths under which forcefield data (.rtf, .prm, .str) are searched if full path is not provided.
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.
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.
Condition that triggers the use of a conditional block. Every conditional block must contain this keyword. The string is evaluated as ruby code.
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.
Out of plane / out of axis displacement (in degrees) for connector types out_of_plane and in_plane.
Distance of teh connector from an atom. Acceptable values are "vdw", "covalent" and a number (distance in A).
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 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.
Coordinate system used for geometry optimization. To use z-matrix, the geometry must be loaded from a z-matrix format.
Convergence threshold for iterative calculations of correlation energy, set to 10^-X a.u.
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.
Interval for scanning the axis between the molecules for the best divider plane. Format is [start, step, end]
Path to directory where cuby stores local data (e.g. cache). The directory must be writeable by user.
Print cycle header before the job is run (useful only for serial jobs).
Name of the keyword whose value is changed (may be omitted if cycle_templates is used).
Mode of printing scan results:
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.
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).
Exponent in damping function in C8 term. If if not setm value of d3_alpha6 + 2 is used.
Elementwise scaling factors applied to the C6 coefficients
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).
Width of the region where dispersion is smoothly swithed off when cutoff is used.
Selection of damping function:
Fix for systems with atoms with valence number significantly higher than in the molecules used to derive the C6 coefficients.
Hydrogen-hydrogen repulsion term for semiempirical methods. Provide parameters using the d3_hh_para keyword.
Parameters for the H-H repulsuion correction for SQM methods. Should contain theree parameters, k, e and r0.
Hybridization used to determine atomic parameters:
Custom values for hybridization numbers used for calculation of geometry-dependent C6 coefficients
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.
Elementwise scaling factors applied to the atomic radii used in the damping function
Version of the D3 pareametrization.
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.
Used when dataset = from_files. List of files to build the dataset from. Shell-like wildcards are allowed.
Used when dataset = from_files. Protocol to be aplied to the items in the data set, 'energy' is the dafault.
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.
Separator between groups in the printed table. By default, no separator is used.
Add extra series to the plots from yaml files. The value should be a hash "name": filename.yaml
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.
List of things to be printed in the output:
Processing of the results before valuation of the errors (the same transformation is applied also to the reference values).
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:
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.
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.
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.
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.
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.
Default buffer radius (in Angstrom). It is also the default value in the DC-DFTB-MD program.
Corrections for non-covalent interactions implemented in the DC-DFTB-MD code
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.
Algorithm for the fragmentation of the system.
Dictionary for automated selection of interfaces for specified method
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.
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.
To be used with Voronoi or Becke population constraint to get the e.g. Voronoi Deformation Density scheme.
Enforce specific orbital phase convention in cDFT coupling (HDA) calculations. Applies only to development version with cDFT.
Constrained DFT (cDFT). Available population schemes are:
Construct initial guess from DFT calculations of fragments. The fragments must be defined in the input.
Maximum L number of auxiliary basis functions during SCF. For deMon version 4.2.5 and above.
If set, energy is calculated on the initial guess of density, no SCF iterations are performed
Setup for spatial population analysis: first atom/selection defining the axis of the plane separator
Setup for spatial population analysis: second atom/selection defining the axis of the plane separator
Setup for spatial population analysis: ratio dividing the distance between atoms A and B
Population scheme dividing the space by a plane. Three parameters should be provided: first reference atom, second reference atom and a ratio
Set when a modified version of demon with special cuby support is used.
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).
This keyword is for development purposes only, it makes it possible to temporarily add keywords without defining them explicitly.
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.
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.
Full 3rd order calculation, when disabled, only diagonal (aka. on-site) contribution is calculated. Requires DFTB+ ver 1.2.1
Half-width of gaussian blur of external point charges. Zero for normal point charges.
Use CM3 charges in SCC. Available only in modified version of the old DFTB program.
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).
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.
By default, SCC-DFTB calculation is performed. Non-SCC calculation can be invoked by setting this keyword to false.
Extra input for DFTB+ in its native input format, inserted into the Hamiltonian block
Activates the H5 hydrogen bond correction (now available only in development version of DFTB+).
Elementwise parameters for the H5 correction. Default values are the ones published for DFTB3/3OB.
Parameter for the H5 correction. Default value is the one published for DFTB3/3OB.
Parameter for the H5 correction. Default value is the one published for DFTB3/3OB.
3rd order DFTB uses derivatives of Hubbard parameter. The default values are those obtained from DFT calculation. The keyword can have following values:
Values of custom Hubbard derivatives - see keyword dftb_hubbard_derivs.
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.
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.
Configuration: path to directories containing the sets of Slater-Koster files
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.
Configuration: Name of the Slater-Koster parameter file set (name of directory in dftb_slko_basepath)
XH electrostatic interaction damping to improve hydrogen bonds. Requires DVTB+ ver 1.1
parameter (exponent) for -->dftb_xh_damping . Default value is taken from paper on the method optimized for use with MIO set.
Override c6 coefficients (unit: same as in the data file, J/nm)
Override element radii from the database with custom values (in Angstrom)
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).
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.
Homogenous external electric filed. Enetered as a cartesian vector (array), in a.u.
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).
Condition applied to matching element list. Possible values:
Handling of calculation directories when existing one is found:
File name template for the expand_series action. The string is evaluated as ruby expression, variable 'i' (counter starting at 0) can be used.
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).
Use higher-order correction (delta CCSD(T)) added to MP2/CBS extrapolated correlation.
Mode of gradient calculation:
Option for the 'rmsd_fit_reorder' for resolving topologically identical atoms:
Occupancy threshold for selcction of FNO orbitals. The default value is identical to the default in Psi4.
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.
File to which the geometries of fragment dimers are saved. If set to empty string, no file is generated.
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.
Mode of fragmentation:
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.
Path to external program freesasa (https://github.com/mittinatten/freesasa) used for surface area calculations.
Build a new geometry displaced in all modes with negative frequencies
Identify negative modes corresponding to a rotation of a small functional group (now supported: methyl) and prepare a geometry displaced in all these modes
Large multidimensional scans can be split to multiple files, this number specifies number of geometries per file.
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).
Energy unit for keyword req_mode_scan_e. The options are:
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:
Multi-dimensional scan in selected modes. If the list of modes is empty, 1D scans for each mode are done instead.
List of extra features to be printed:
Set custom frozen core for each element. When not set, turbomole's default is used. When set, values for all elements must be provided.
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.
Custom DFT functional specification in the format used by the intrfaced program.
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 executable version, the default value '00' should work for a normal installation.
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.
Automatic determination of charge for amino acid residues in protein. For other residues, charges can be defined using keyword gamess_fmo_res_charge.
List of fragment charges (fragment number: charge), fragments not on the list are considered neutral.
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.
Define PCM radii for elements that do not have default values. The radii provided here are scaled by the default facor of 1.2.
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.
Job specification, in the gaussian format (e.g. "opt" for optimization, "freq" for frequencies etc.) This is used to construct the input.
When set, cuby writes the results also in a form readable by gaussian when it is used as a driver for external calculations (see http://gaussian.com/g_tech/g_ur/k_external.htm). Supported by protocols Energy, Gradient and Hessian.
Additional block (or blocks, separated by new line) of gaussian input inserted into teh constructed input after the geometry.
Extra keywords in Gaussian format to be appended to the method specification line
Run the GDMA distributed multipole analysis on the Gaussian output (requires a separte tool)
Gaussian version, e.g. "g09" - the version name should correspond to the name of the program binary.
File used to save the generated geometries (.xyz file)
Fitting procedure in measuring the RMSD between geometries in clustering.
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.
Directory for processed geometries. It it does not exist, it will be created.
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.
Action to be performed on the geometry in addition to the standard geometry processing:
Some actions might work on specified selections, by default, all atoms are selected
Keyword providing multiple selections to rmsd_fit_subset action
Break the intermolecular symmetry by twisting the dimer around its axis and bending it out of axis sligtly.
Connect the fragments with a covalent bond, remove the connectors
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).
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).
Reference distance (corresponding to scaling factor 1.0) for the scan.
Connector selection for action connect. Applied to geometry. Value "auto" can be used to read the connector info from .xyz file comment line.
Connector selection for action connect. Applied to geometry2. Value "auto" can be used to read the connector info from .xyz file comment line.
Override vdW radii for some elements. Appliucable in geometry actions:
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.
Atomic charges to be loaded into the geometry (reads the format produced by Cuby).
Distance limit (a scaling factor applied to vdw radii) used for selection of noncovalent interactions by the list_nc_... actions.
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.
Max. random displacement (in Angstrom) applied to each coordinate by geometry actions randomize and random_translation.
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.
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.
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.
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.
List of z-matrix coordinates updated after reading the geometry
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.
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 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.
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"
Following z-matrix formats are availbale:
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.
Calculate and print also the gradient on point charges. The gradient projection should be switched off.
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.
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.
Parameters for the H-bond correction. By default, parameters for the selected method are loaded automatically.
Skip corerction for specific acceptor arrangement. Following cases are supported:
Estimate of the initial hessian. It applies only to optimizations in redundant internal coordinates with quasi-Newton optimizers. The values are:
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.
File name of the Hessian to be read (yaml format). If not specified or empty (default value), the Hessian is calculated.
File to write the calculated Hessian to. If the string is empty, Hessian is not written.
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.xyz".
If set, additional history file is written for a atoms selected by this keyword.
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.
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.
File with a lookup table used for the construction of the estimate of the initial Hessian.
Check for atoms missing in selections of molecule_a and molecule_b.
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 type (calculation protocol). The available protocols are listed in the documenation (page Protocols on the website, accessible from commandline by running 'cuby4 protocol').
Linesearch
A list of measuremens to be done, as a name: expression hash. For available measuremet expressions, see the documentation of the protocol 'measure'.
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.
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).
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.
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.
Allows limiting the value of the maxcor input separately for SCF (in MB). Applied only when set, recommended value is 500.
When enabled, the internal queue system of cuby identifies duplicate calculations and calculates them only once.
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...
Weight for calculation a. The calculation should be defined in a block calculation_a.
Weight for calculation a evaluated as ruby expression. Overrides the numeric value provided in mixer_weight_a.
Weight for calculation a. The calculation should be defined in a block calculation_a.
Weight for calculation a evaluated as ruby expression. Overrides the numeric value provided in mixer_weight_b.
A list of interfaces applied as a modifiers to this calculations. Setup for each modifier should be provided in a block modifier_modifiername.
Molpro license key. It has to be set only when Molpro can not find the key it was installed with.
Path to the directory containingi basis set libraries etc. needed by Molpro (set using the -L commandline option).
Level of density fitting in DFT-SAPT. Values from 0 (no DF) to 3 (most approximate).
Corrections for noncovalent interactions for PM6 as implemented in MOPAC.
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.
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.
Van der Waals radii for COSMO. Hash element: radius.
Allows modification of the semiempirical parameters from cuby input. When set, the keyword EXTERNAL is added to the input automatically.
Use of the linear scaling MOZYME algorithm. MOPAC documentation: http://openmopac.net/manual/mozyme.html
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.
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: http://openmopac.net/manual/mmok.html
Use tight thresholds, needed for accurate gradient. MOPAC documentation: http://openmopac.net/manual/precise.html
Relative accuracy of SCF calculation (multiplier for convergence thresholds) passed to RELSCF keyword.
Manual specification atomic charges for MOZYME, hash of charges indexed by atom selection. The charge can be '0', '+' or '-'. Described at http://openmopac.net/manual/Labels.html
Manual specification of double bonds for MOZYME, array of atom pairs (defined by two selection expressions separated by semicolon). MOPAC documentation: http://openmopac.net/manual/setpi.html
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.
Attempt restarting coupled clusters, skipping SCF step. Restart and integral files from a previous run must be present.
Spin multiplicity - required for all QM calculations. If not set, a default value 1 is used silently.
Alternatively to multistep_result_expression, a piece of ruby code can be called on the results. For experts only.
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.
Name of the result calculated using multistep_result_expression keyword
Force constant of the harmonic potential connecting the points on the elastic band (kcal/mol/A).
The file to which the minimum energy path is written to. It is updated in each step.
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.
Optimization of the end points of the MEP can be disabled if the provided geometries are already optimized.
Version of the formulation of the NEB, see the references in the documentation.
Optional calculation of the derivatives of the atomic charges.
Number of points per atom used for numerical differentiation:
The size of the displacemeni (in Angstrom) used in the numerical differentiation.
Number of points per atom used for numerical differentiation:
When enabled, restart file 'auto_restart.xyz' 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.
Convergence limit for energy change between steps (kcal/mol). If set to 0, this criterium is not evaluated.
Convergence limit for maximum gradient component (kcal/mol/A). If set to 0, this criterium is not evaluated.
Convergence limit for root mean square of gradient (gradient norm) (kcal/mol/A). If set to 0, this criterium is not evaluated.
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")
Hessian update formula for quasi-Newton optimizers
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.
Step size scaling mode for RFO, QN and LBFGS (TRIM uses another means of step size control):
Optional printing:
Optimization to transition state. Available only in optimization using Hessian calculated in each step.
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.
Dispersion corrections calculated in Orca.
Enable the Domain-localized pair natural orbitals approximation in CCSD and CCSD(T) calculation.
DLPNO thresholds (loose/normal/tight). If the value "custom" is used, the thresholds can be manually defined using orca_extra_input keyword.
Pseudopotentials. When set to 'auto', ORCA assigns pseudopotentials automatically fot the selected basis sets.
Guess for starting SCF. When not set, Orca's default is used
Additional keywords passed to ORCA, in the simple format (a line beginning with !)
Orca native optimization convergence limit in terms of step size (max and rms) (a.u.)
Orca native optimization convergence limit in terms of energy change (a.u.)
Orca native optimization convergence limit in terms of gradient (max and RMS) (a.u.)
Use the RIJCOSX (RI-J chain of spheres) approximation for HF exchange calculation.
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.
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.
Mode of parallel execution of the external software. Use the value 'default' unless the external program supports multiple options. The options are:
Controls printing of additional columns in PDB files (beyond coordinates). Applicable to all tasks where PDB file is written.
Renaming of PDB residues. Hash in form atom_selection: new_name.
Switches on periodic boundary conditions. Note that this is supported by only very few interfaces.
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.
The origin of the periodic box in the cartesian coordinates can be set by this keyword. The default is the origin ([0,0,0]).
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.
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.
List of extra features to be printed:
Calculation of additional properties
Specification of pseudopotentials for selected elements. The format is a hash element: "pseudopotential_name"
Separate fragments in DFT geometry. Two fragments should be defined in blocks molecule_a and molecule_b. Keywords charge, multiplicity and selection are needed.
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.
Switch on additional SAPT calculations to separating charge transfer energy as a difference between SAPT polarization in monomer and dimer basis.
Selection of atoms in QM regieon (selection expression) after which PDB TER labels are added.
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.
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.
The "embedding" used:
If set, the program is aborted after preparation of the QM region but before the calculations are prepared.
Name of the file to which geometry is written to. Set to empty string to prevent writting this file.
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.
List of residues to be renamed in QM region. Format: YAML array of strings "selection new_name".
Number of waters in the QMMM regions (waters clostest to the center defined by qmmm_wat_center are selected)
Additional comands to be inserted into the shell script that executes cuby on the node - useful for e.g. seting up the environment.
Number of nodes to be allocated. Note that parallelization across nodes is not supported by most cuby interfaces.
Number of CPUs allocated in the queue system (per node). If not set, it is calculated from other keywords as parallel * cuby_threads
Additional commandline options for the command submitting the job (usually named qsub).
Directory where the results are put to after job finishes. Path is relative to the directory in which the job is submitted.
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.
Submit the job to queue instead of running it immediately. The submission system must be configured accordingly.
Queue system used:
Random seed used to initialize the random number generator when setting up a MD run. When not set, random initialization is used.
List of geometries of all molecules, in the order they are presented in the formula
Controls the output of the protocol. Allowed options are:
Generate the geometries of the molecules using SMILES notation from the formula itself
Freeze some class of internal coordinates
Allows to reduce frozen shells per element, for use with pseudopotentials.
Mode of parallel (specified by -->cuby_threads) remote execution of calcualtions. The options are:
List of URIs of the remote servers (the URI is printed when the server is started)
Specifies how the calculation files are transferred to a node:
Removes rotational component of a gradient in each cycle of optimization or MD a velocity in MD simulation.
Removes translational component of a gradient in each cycle of optimization or a velocity in MD simulation.
Replace the total energy in the result with a selcted component of it. The original energy is stored in a component "original_energy".
Replace the total energy with a result of a ruby eval call - the result can be constructed from any other varibles.
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".
Name of file to which the last geometry is written. When not specified, the name of the file is "optimized.xyz" if the job is an optimization and it has converged, and "last.xyz" if it did not. For MD, the default is also "last.xyz". Setting the value to "" means no restart file is written.
By default, the restart file is overwritten, use this option to append the coordinates to an existing file
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.
Selection of atoms the restraints are applied to. By default, all atoms in the geometry are selected.
List of restraints. Each line has format: distance|angle|torsion|distance_difference; value; force_constant; atom_selection1; atom_selection2; ... Angles are specified in degrees
Three angles (in degrees) for rotation in cartesian space, as three comma-separated values
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.
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.
Setup for the scan generator. Different options are available for different generators, see the protocol documentation.
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.
Mode of printing scan results:
Integral storage in SCF. When not set, the default option of the interfaced program is used. The other options are:
Shift of virtual orbitals (in a.u.). When the keyword is not set, default value of the external program is used.
Atom selection using cuby's selection language. The default value is context-dependent:
Run SCF part of calculation in serial and paralellize only the correlation part.
Commands to be executed in the default shell (using the system call from ruby).
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'.
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)
In some programs, the solvent is specified by its name - see the respective documentation.
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); http://dx.doi.org/10.1063/1.1809602
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).
SCS scaling in MP2. Use scs_ss and scs_ss keywords to set the scaling coefficients.
Restricted/Unrestricted spin treatment. The value 'auto_uhf' swiches on UHF for any open-shell system while RHF is used for closed shells.
Use results from previous step (of, e.g. geometry optimization) as a starting point for the calculation
When set in a step block, the calculation is queued until a following steps triggers execution of the queue
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.
Add also the geometry to the results object - useful when combined with 'write_results_yaml'
Path to external program symmol (http://www.ccp14.ac.uk/ccp/web-mirrors/symmol/~pila/) used for symmetry determination / symmetrization.
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.
The result the tested calculation should yield. The value is converted to and tested as quantity defined by keyword test_result_type.
Type of the result tested:
Special treatment of low frequency modes in thermodynamics calculations:
Pressure for the thermodynamics calculations, in Pa. The default is 1 atm.
Thermostat time constant (ps) setting strength of the coupling to the thermostat. The exact mening of the value is different in different algorithms.
A lookup for parallel_mode == default which allows specifying paralellization mode (mpi, shm, omp) for individual turbomole modules.
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.
Format of the trajectory:
Frequency of writing the trajectory (every Nth step). If set to 0, no trajectory is written.
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).
Upper limit of trust_radius when dynamic change of it is allowed (by opt_tr_update)
Lower limit of trust_radius when dynamic change of it is allowed (by opt_tr_update)
Sets maximum number of CCSD iterations. When not set, turbomole uses its default value.
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.
Save system information (disk space, etc...) before each call of a turbomole binary
Calculate and save a separate SCF gradient before post-HF gradient is calculated.
Apply the RI approximation also to Coulomb integrals (RI-JK) method, instead of just exchange (RI-J).
Multipole-accelerated resolution of identity approximation for HF/DFT calculation. Turbomole's default setup is used.
Skip the SCF step. This allows running additional correlation calculation on an independently performed SCF calculation.
Assignment of initial velocities. The options are:
Verbosity of the output:
Center of the waterball:
Selection defining the solute or the center of solvation in it. Required when waterball_center is set to solute or fixed_solute
Force constant of the restraint holding the solute close to the origin of the coordinate system, applies only to waterball_center = fixed_solute
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".
When set, covalent bonds and 1-3 and 1-4 covament neigbors are excluded from the corrected 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 directory (should contain parameter files and binary in 'bin' subdirecory).
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.
Selection of the coordinates displaced using displacement_in_zmat. The *_im options apply only to intermolecular coordinates.