Options

[ff]

n_equiv, int:

default: 4
Number of n equivalent neighbors needed to consider two atoms equivalent
Negative values turns off equivalence, 0 makes same elements equivalent 

n_excl, int:

default: 2, from Choices(2, 3)
Number of first n neighbors to exclude in the forcefield 

lennard_jones, str:

default: opls_auto, from Choices(gromos_auto, gromos, opls_auto, opls, gaff, gaff2, charmm36, ext)
Lennard jones method for the forcefield 

ext_charges, bool:

default: False, from Choices(True, False)
Use externally provided point charges in the file "ext_q" in the job directyory 

charge_scaling, float:

default: 1.2
Scale QM charges to account for condensed phase polarization (should be set to 1 for gas phase) 

use_ext_charges_for_frags, bool:

default: False, from Choices(True, False)
If user chooses ext_charges=True, by default fragments will still use the chosen QM method for
determining fragment charges. This is to avoid spuriously high charges on capping hydrogens.
However, using QM charges for fragments and ext_charges for the molecule can also result in
inaccuracies if these two charges are very different. 

ff::exclusions, LiteralBlock

Additional exclusions (GROMACS format) 

ff::pairs, LiteralBlock

Switch standard non-bonded interactions between two atoms to pair interactions
(provide atom pairs in each row) 

ext_lj_lib, folder:

Path for the external FF library for Lennard-Jones parameters (GROMACS format). 

ext_lj_fudge, float:

Lennard-Jones fudge parameter for 1-4 interactions for when "lennard_jones" is set to "ext". 

ext_q_fudge, float:

Coulomb fudge parameter for 1-4 interactions for when "lennard_jones" is set to "ext". 

ext_comb_rule, int:

Choices(1, 2, 3)
Lennard-Jones combinations rules for when "lennard_jones" is set to "ext" (GROMACS numbering). 

ext_h_cap, str:

Name of the atom type for capping hydrogens for when "lennard_jones" is set to "ext" 

all_rigid, bool:

default: False, from Choices(True, False)
Set all dihedrals as rigid (no dihedral scans) 

res_name, str:

default: MOL
Residue name printed on the force field file (Max 5 characters) 

ff::_polar_not_scale_c6, LiteralBlock

Specifically not scale some of the atoms 

[qm]

software, str:

default: gaussian, from Choices(gaussian, qchem, orca, xtb)
QM software to use 

qm::job_script, LiteralBlock

To turn the QM input files into job scripts 

scan_step_size, float:

default: 15.0
Step size for the dihedral scan (360 should be divisible by this number ideally) 

charge, int:

default: 0
Total charge of the system 

multiplicity, int:

default: 1
Multiplicity of the system 

memory, int:

default: 4000
Allocated memory for the QM calculation (in MB) 

n_proc, int:

default: 1
Number of processors to set for the QM calculation 

vib_scaling, float:

default: 1.0
Scaling of the vibrational frequency for the corresponding QM method (not implemented) 

dihedral_scanner, str:

default: relaxed_scan, from Choices(relaxed_scan, xtb-torsiondrive)
Use the internal relaxed scan method of the QM software or the Torsiondrive method using xTB 

[qm::software(gaussian)]

charge_method, str:

default: cm5, from Choices(cm5, esp) 

method, str:

default: PBEPBE
QM method to be used 

dispersion, str:

default: EmpiricalDispersion=GD3BJ
Dispersion method - leave it empty to turn off 

basis, str:

default: 6-31+G(D)
QM basis set to be used - leave it empty to turn off 

solvent_method, str:

Include implicit solvent for the complete parametrization 

[qm::software(orca)]

charge_method, str:

default: esp, from Choices(cm5, esp) 

qm_method_opt, str:

default: r2SCAN-3c
QM method to be used for geometry optimisation 

qm_method_hessian, str:

default: B3LYP D4 def2-TZVP def2/J RIJCOSX
QM method to be used for hessian calculation
Note: The accuracy of this method determines the accuracy of bond,
angle and improper dihedral. 

qm_method_charge, str:

default: HF 6-31G*
QM method to be used for charge derivation
Note: Method chosen according to the standard RESP procedure. 

qm_method_sp, str:

default: PWPB95 D4 def2-TZVPP def2/J def2-TZVPP/C notrah RIJCOSX tightSCF
QM method to be used for dihedral scan energy calculation.
Note: The accuracy of this method determines the accuracy of
flexible dihedral. 

[qm::software(qchem)]

charge_method, str:

default: cm5, from Choices(cm5, resp) 

method, str:

default: PBE
QM method to be used 

dispersion, str:

default: d3_bj, from Choices(d3, d3_bj, d3_bjm, d3_zero, d3_op, empirical_grimme)
Dispersion (enter "no"/"false" to turn off) 

basis, str:

default: 6-31+G(D)
QM basis set to be used (enter "no"/"false" to turn off) 

max_scf_cycles, int:

default: 100
Number of maximum SCF cycles 

max_opt_cycles, int:

default: 100
Number of maximum optimization cycles 

xc_grid, int:

default: 3, from Choices(0, 1, 2, 3)
DFT Quadrature grid size 

cis_n_roots, int:

Number of CIS roots to ask 

cis_singlets, bool:

Choices(True, False)
CIS singlets turned on or off 

cis_triplets, bool:

Choices(True, False)
CIS triplets turned on or off 

cis_state_deriv, int:

Sets CIS state for excited state optimizations and vibrational analysis 

solvent_method, str:

Include implicit solvent for the complete parametrization 

[qm::software(xtb)]

charge_method, str:

default: xtb
xTB only allows Mulliken charge. 

xtb_command, str:

default: --gfn 2
Extra command line passed to the xtb executable 

[scan]

do_scan, bool:

default: True, from Choices(True, False)
Perform dihedral scan for flexible dihedrals 

avail_only, bool:

default: False, from Choices(True, False)
Skip dihedrals with missing scan data and accept scan data that is missing data points.
False: Exit if scan data for a dihedral is missing or if it has missing data points) 

frag_threshold, int:

default: 3
Number of neighbors after bonds can be fragmented (0 or smaller means no fragmentation) 

break_co_bond, bool:

default: False, from Choices(True, False)
Break C-O type of bonds while creating fragments (O-C is never broken) 

method, str:

default: qforce, from Choices(qforce, gromacs)
Method for doing the MM relaxed dihedral scan 

gromacs_exec, str:

default: gmx
The executable for gromacs - necessary if scan method is gromacs 

n_dihed_scans, int:

default: 5
Number of iterations of dihedral fitting 

scan::symmetrize, LiteralBlock

Symmetrize the dihedral profile of a specific dihedral by inputting the range
For symmetrizing the dihedral profile between atoms 77 and 80 where 0-180 is inversely
equivalent to 180-360:
77 80 = 0 180 360 : +- 

plot_fit, bool:

default: False, from Choices(True, False)
Save extra plots with fitting data 

frag_lib, folder:

default: /home/docs/qforce_fragments
Directory where the fragments are saved 

batch_run, bool:

default: False, from Choices(True, False)
Skip the dihedrals that are generated but not computed 

[terms]

urey, bool:

default: True, from Choices(True, False)
Turn urey FF term on or off 

dihedral/rigid, bool:

default: True, from Choices(True, False)
Turn dihedral/rigid FF term on or off 

dihedral/improper, bool:

default: True, from Choices(True, False)
Turn dihedral/improper FF term on or off 

dihedral/flexible, bool:

default: True, from Choices(True, False)
Turn dihedral/flexible FF term on or off 

dihedral/inversion, bool:

default: True, from Choices(True, False)
Turn dihedral/inversion FF term on or off 

non_bonded, bool:

default: True, from Choices(True, False)
Turn non_bonded FF term on or off