Parameter files


The static properties (see Table 11) assigned to the atom types are assigned based on data in several places. The mass is listed in atomtypes.atp (see Atom types), whereas the charge is listed in rtp (rtp = residue topology parameter file, see rtp). This implies that the charges are only defined in the building blocks of amino acids, nucleic acids or otherwise, as defined by the user. When generating a topology using the pdb2gmx program, the information from these files is combined.

Table 11 Static atom type properties in GROMACS
Property Symbol Unit
Mass m a.m.u.
Charge q electron
epsilon \(\epsilon\) kJ/mol
sigma \(\sigma\) nm

Non-bonded parameters

The non-bonded parameters consist of the van der Waals parameters V (c6 or \(\sigma\), depending on the combination rule) and W (c12 or \(\epsilon\)), as listed in the file ffnonbonded.itp, where ptype is the particle type (see Table 10). As with the bonded parameters, entries in [ *type ] directives are applied to their counterparts in the topology file. Missing parameters generate warnings, except as noted below in section Intramolecular pair interactions.

[ atomtypes ]
;name   at.num      mass      charge   ptype         V(c6)        W(c12)
    O        8  15.99940       0.000       A   0.22617E-02   0.74158E-06
   OM        8  15.99940       0.000       A   0.22617E-02   0.74158E-06

[ nonbond_params ]
  ; i    j func       V(c6)        W(c12)
    O    O    1 0.22617E-02   0.74158E-06
    O   OA    1 0.22617E-02   0.13807E-05

Note that most of the included force fields also include the at.num. column, but this same information is implied in the OPLS-AA bond_type column. The interpretation of the parameters V and W depends on the combination rule that was chosen in the [ defaults ] section of the topology file (see Topology file):

(1)\[\begin{split}\begin{aligned} \mbox{for combination rule 1}: & & \begin{array}{llllll} \mbox{V}_{ii} & = & C^{(6)}_{i} & = & 4\,\epsilon_i\sigma_i^{6} & \mbox{[ kJ mol$^{-1}$ nm$^{6}$ ]}\\ \mbox{W}_{ii} & = & C^{(12)}_{i} & = & 4\,\epsilon_i\sigma_i^{12} & \mbox{[ kJ mol$^{-1}$ nm$^{12}$ ]}\\ \end{array} \\ \mbox{for combination rules 2 and 3}: & & \begin{array}{llll} \mbox{V}_{ii} & = & \sigma_i & \mbox{[ nm ]} \\ \mbox{W}_{ii} & = & \epsilon_i & \mbox{[ kJ mol$^{-1}$ ]} \end{array}\end{aligned}\end{split}\]

Some or all combinations for different atom types can be given in the [ nonbond_params ] section, again with parameters V and W as defined above. Any combination that is not given will be computed from the parameters for the corresponding atom types, according to the combination rule:

(2)\[\begin{split}\begin{aligned} \mbox{for combination rules 1 and 3}: & & \begin{array}{lll} C^{(6)}_{ij} & = & \left(C^{(6)}_i\,C^{(6)}_j\right)^{\frac{1}{2}} \\ C^{(12)}_{ij} & = & \left(C^{(12)}_i\,C^{(12)}_j\right)^{\frac{1}{2}} \end{array} \\ \mbox{for combination rule 2}: & & \begin{array}{lll} \sigma_{ij} & = & \frac{1}{2}(\sigma_i+\sigma_j) \\ \epsilon_{ij} & = & \sqrt{\epsilon_i\,\epsilon_j} \end{array}\end{aligned}\end{split}\]

When \(\sigma\) and \(\epsilon\) need to be supplied (rules 2 and 3), it would seem it is impossible to have a non-zero \(C^{12}\) combined with a zero \(C^6\) parameter. However, providing a negative \(\sigma\) will do exactly that, such that \(C^6\) is set to zero and \(C^{12}\) is calculated normally. This situation represents a special case in reading the value of \(\sigma\), and nothing more.

There is only one set of combination rules for Buckingham potentials:

(3)\[\begin{split}\begin{array}{rcl} A_{ij} &=& \left(A_{ii} \, A_{jj}\right)^{1/2} \\ B_{ij} &=& 2 / \left(\frac{1}{B_{ii}} + \frac{1}{B_{jj}}\right) \\ C_{ij} &=& \left(C_{ii} \, C_{jj}\right)^{1/2} \end{array}\end{split}\]

Bonded parameters

The bonded parameters (i.e. bonds, bond angles, improper and proper dihedrals) are listed in ffbonded.itp.  The entries in this database describe, respectively, the atom types in the interactions, the type of the interaction, and the parameters associated with that interaction. These parameters are then read by grompp when processing a topology and applied to the relevant bonded parameters, i.e. bondtypes are applied to entries in the [ bonds ] directive, etc. Any bonded parameter that is missing from the relevant :[ *type ] directive generates a fatal error. The types of interactions are listed in Table 14. Example excerpts from such files follow:

[ bondtypes ]
  ; i    j func        b0          kb
    C    O    1   0.12300     502080.
    C   OM    1   0.12500     418400.

[ angletypes ]
  ; i    j    k func       th0         cth
   HO   OA    C    1   109.500     397.480
   HO   OA  CH1    1   109.500     397.480

[ dihedraltypes ]
  ; i    l func        q0          cq
 NR5*  NR5    2     0.000     167.360
 NR5* NR5*    2     0.000     167.360

[ dihedraltypes ]
  ; j    k func      phi0          cp   mult
    C   OA    1   180.000      16.736      2
    C    N    1   180.000      33.472      2

[ dihedraltypes ]
; Ryckaert-Bellemans Dihedrals
; aj    ak      funct
CP2     CP2     3       9.2789  12.156  -13.120 -3.0597 26.240  -31.495

In the ffbonded.itp file, you can add bonded parameters. If you want to include parameters for new atom types, make sure you define them in atomtypes.atp as well.

For most interaction types, bonded parameters are searched and assigned using an exact match for all type names and allowing only a single set of parameters. The exception to this rule are dihedral parameters. For [ dihedraltypes ] wildcard atom type names can be specified with the letter X in one or more of the four positions. Thus one can for example assign proper dihedral parameters based on the types of the middle two atoms. The parameters for the entry with the most exact matches, i.e. the least wildcard matches, will be used. Note that GROMACS versions older than 5.1.3 used the first match, which means that a full match would be ignored if it is preceded by an entry that matches on wildcards. Thus it is suggested to put wildcard entries at the end, in case someone might use a forcefield with older versions of GROMACS. In addition there is a dihedral type 9 which adds the possibility of assigning multiple dihedral potentials, useful for combining terms with different multiplicities. The different dihedral potential parameter sets should be on directly adjacent lines in the [ dihedraltypes ] section.