The parameter set used by UFF can be changed via the
Library [UFF | UFF4MOF | UFF4MOF-II]
Type: Multiple Choice Default value: UFF Options: [UFF, UFF4MOF, UFF4MOF-II] Description: Selects the used parameter library.
Aside from the standard UFF forcefield, we ship two parameter sets for Metal-Organic Frameworks:
We ship the extended parameter set for Metal-Organic Frameworks created by M.A. Addicoat et al. (2013). Select the UFF4MOF_general_db, UFF4MOF_elements_db and UFF4MOF_mmatomtypes_db files to use these parameters, and check that the proper atom types are detected for your system or set them manually. Please see  for details on the parameters.
We ship a second extended parameter set for Metal-Organic Frameworks created by D.E. Coupry et al. (2016). Select the UFF4MOFII_general_db, UFF4MOFII_elements_db and UFF4MOFII_mmatomtypes_db files to use these parameters, and check that the proper atom types are detected for your system or set them manually. Please see  for details on the parameters.
User-modified force fields (expert option)¶
Finding good UFF parameters can be a challenging task, and any results with modified parameters should be checked very carefully. SCM has no experience with this, and the parameters supplied for UFF have not been generated by us. Feel free to test new parameters, and feel free to let us know if you have a good working set for a specialized situation.
General parameters file
Type: String Default value: general_db Description: Expert option: Select the file that defines the UFF parameters per atom type
The general_db file ($ADFHOME/atomicdata/UFF/general_db) contains all the parameters used to calculate the forces and energies. The format is:
MMAtomType, ri, phi, xi, di, psi, zmm, vsp3, vsp2, chi, nc.
The items in the list are:
- MMAtomType: name, max 5 characters
- ri: Valence Bond [Å]
- phi: Valence Angle [Degree]
- xi: Nonbond Distance [Å]
- di: Nonbond Energy [kcal/mol]
- psi: Nonbond scale [Number]
- zmm: Effective Charge [Charge]
- vsp3: sp3 Torsional Barrier [kcal/mol]
- vsp2: sp2 Torsional Barrier [kcal/mol]
- chi: Electronegativity
- nc: Number of directly attached atoms, aka coordination number. This is required for counting the number of possible dihedrals, and is defined only for the sp2 and sp3 centers (types 2, R, and 3)
The current set of parameters comes from the deMonNano program, and is a combination of published parameters and fitted data to fill in the gaps. The deMonNano documentation says the following about the parameters:
Implementation of the Universal Force Field (UFF) in deMonNano -------------------------------------------------------------- As far as possible, UFF molecular mechanics forcefield in deMon follows the published forcefield definition in . In several cases, the definitions and expressions in  are not consistent with the published applications of the forcefield [1,5,6]. In those cases, an attept was made to correct the errors and omissions, using information from . The following changed were made, compared to the published UFF forcefield description (all equation and page numbers refer to ). 1. Sign error in Eq. 2 (equilibrium bond length) was corrected - electronegativity correction must be negative! 2. Equilibrium valence angle for O_3_z was corrected from 146.0 degree to 145.45 degree. 3. Bending periodicity (Eq. 10) for linear coordination was corrected from 1 to 2. 4. Sign errors were corrected in eqs. 13 and and unnumbered equation for the beta parameter (between eqs. 13 and 14). 5. The reference value of the UFF amide force constant, of 105.5 kcal/mol/rad**2 (p. 10028) is wrong. The results are consistent with the force constant of 211.0 kcal/mol/rad**2. 6. Equilibrium torsional angle for a bond between a group-6A atom (oxygen ...) and an sp2 atom (90 degree) is wrong (p. 10028). It should be 0 degree. 7. The conditional for the special-case sp2-sp3 torsion (p. 10029) is wrong, and should be inverted - see . 8. The overall shape of the UFF torsional potential degenerates to a Heavyside function when one of the bond angles becomes linear, leading to failures in geometry optimization and force constant evaluation. The UFF torsional term was augmented with a smooth masking function, to avoid this. See "uff_4centre.f90" for details. 9. UFF inversion potential is not defined in  for group 5A elements (from phosphorus down). Taking the equilibrium inversion coordinate of 87 degree, and the suitable expressions for the cosine weights (see uff_get_inversion_shape in "uff_database.f90") appears to reproduce published UFF structures and energetics. The following atom types have been fully tested, and are believed to reproduce published UFF forcefield results exactly. The examples refer to the $deMon/examples/test.mm directory. Atom type Example Description --------- ------- ----------- Al3 alme3tma Trivalent aluminum As3+3 asf3 Trivalent arsenic B_2 bcl3 Planar (sp2) boron B_3 b2h5nme2 Tetrahedral (sp2) boron, including charge transfer adducts and borohydrates Br bbr3 Univalent bromine C_1 c2h2, co Linear (sp) carbon C_2 acetone Planar tricoordinated (sp2) carbon C_3 c2h6 Tetrahedral (sp3) carbon C_R c4h6 Resonant, variable bond order (sp2) carbon. Cl socl2 Univalent chlorine F_ sof2ncl Univalent fluorine Ge3 geh3ogeh3 Tetrahedral (sp3) germanium H_ h2o Normal, non-bridging hydrogen H_b b2h5nme2 Bridging hydrogen, for use in boranes (NOT SUITABLE FOR H-BONDS!) I_ bi3 Univalent iodine N_1 ch3cn Monocoordinated (sp) nitrogen, triple bond N_2 ch3n2ch3 Dicoordinated (sp2) nitrogen, single-double bond N_3 ch3nh2 Amine (sp3) nitrogen, three single bonds N_3+4 b2h5nme2 Charged amine (sp3) nitrogen, four single bonds (THIS IS NOT A STANDARD UFF TYPE!) N_R c5h5n Resonant planar (sp2) nitrogen, for use in aromatics and amides. For amides, use 1.41 bond order! O_1 co Special "co" type, one triple bond. O_2 acetone One-coordinated (sp2) oxygen, one double bond. O_3 h2o Two-coordinated (sp3) oxygen, two single bonds O_3_z sih3osih3 Special two-coordinated oxygen, for use in Si-O bonds O_R c4h4o Resonant planar (sp2) oxygen, also for use in nitro groups and such. P_3+3 ph3 Pyramidal (sp3) phosphorus, three single bonds P_3+5 p4o7 Tetrahedral hypervalent phosphorus P_3+q bh3ph3 Dative tetrahedral (sp3) phosphorus, watch for the bond order! S_3+2 ch3sch3 Bent two-coordinated sulfur (sp3), two single bonds S_3+4 socl2 Pyramidal three-coordinated hypervalent sulfur S_3+6 so2cl2 Tetrahedral four-coordinated hypervalent sulfur Se3+2 h2se Bent two-coordinated (sp3) selenium Si3 si4o4h8 Tetrahedral silicon Additionally, parameter sets for the following atom types are believed be complete, and may be expected produce results identical to the published UFF data: Li, Na, K_, Rb, Cs (Note that UFF does not specify atomic charges - it is your responsibility to assign those, if charges are needed!) For the remaining atom types, UFF definition  relies on an unpublished set of electronegativities . In deMon, these values were replaced by Pauling electronegativities, scaled to fit published UFF electronegativities. This can be expected to produce small deviations in bond lengths and bond angles, compared to published UFF results.
If you wish to use other parameters, you should copy the general_db file, and rename it. This new file can also be placed outside of $ADFHOME/atomicdata/UFF.
Type: String Default value: elements_db Description: Expert option: Select the file that defines the elements known to UFF
The elements_db file holds all the elements known to UFF. Keep in mind that these are not the MMAtomTypes, but pure chemical elements. The table contains for every element: atomic number, symbol, minimal valence number, maximum valence number, minimal bond order, maximal bond order. The data in the elements_db is mainly used for cleaning up the Pauling bond orders guessed by UFF, and will probably not need to be modified.
MM Atom Types file
Type: String Default value: mmatomtypes_db Description: Expert option: Select the file that defines how UFF determines the atom types
The mmatomtypes_db file contains the matching rules for assigning MM atom types to chemical elements, based on their valence number, and the number of neighbor (bonded) atoms. The current implementation of UFF is limited to 6 MM atom types per element. The table contains for every MM atom type: Number of the element it belongs to, the i-th type of this element, the valence number corresponding to this MM atom type, number of neighbors this MM atom type has, the name of this MM atom type. The naming convention follows the original UFF paper :
A five-character mnemonic label is used to describe the atom types. The first two characters correspond to the chemical symbol; an underscore appears in the second column if the symbol has one letter (e.g.,
N_ is nitrogen,
Rh is rhodium). The third column describes the hybridization or geometry: 1 = linear, 2 = trigonal, R = resonant, 3 = tetrahedral, 4 = square planar, 5 = trigonal bipyramidal, 6 = octahedral. Thus N_3 is tetrahedral nitrogen, while Rh6 is octahedral rhodium. The forth and fifth columns are used as indicators of alternate parameters such as formal oxidation state: Rh6+3 indicates an octahedral rhodium formally in the +3 oxidation state, e.g., Rh(NH3)_6^3+. H_b indicates a bridging hydrogen as in B2Hs O_3_z is an oxygen suited for framework oxygens of a zeolite lattice. P_3_q is a tetrahedral four-coordinate phosphorus used to describe organo-metallic coordinated phosphines.
You can copy the mmatomtypes_db and change it if you need to modify the atom typing behavior of UFF.