Setup Files
The following setup files can be given as additional input to PQ. The names of the used files need to be provided with the according
Setup File Keys in the .in file if the name does not match the default name.
Moldescriptor
Default Name: moldescriptor.dat
The moldescriptor file is used to assign every atom in the system to a molecular unit, also called moltype. These molecular units can be as small
as just a single atom or as big as a whole molecule. They are numbered consecutively starting from 1 and are given in the third column of
the .rst file as described in the Restart File section. The moldescriptor file is structured into groups for every moltype,
which have the following form:
line 1: name n_atoms chargeline 2 to (n_atoms + 1): atom_type_name atom_type_index point_charge global_vdW_index
The parameters name, n_atoms, and charge in the first line denote the name of the moltype, the number of atoms in the moltype, and the total charge of the moltype in units of the elementary charge e. The following lines contain the name of the atom type, the index of the MM atom type, the MM point charge in units of e and the global van der Waals index for each atom in the moltype. The atom type name is irrelevant for internal calculations, but will be printed to various Output Files. The index of the atom type is relevant for defining intra- and intermolecular non-bonded interactions in the GUFF File. The point charge as well as the global van der Waals type are only relevant for MM atoms that are not treated via the GUFF File. The global van der Waals index is used to assign identical elements exposed to a similar chemical environment from different moltypes to the same atom type.
Attention
Providing a moldescriptor file is optional for pure QM calculations, but becomes mandatory if there are MM atoms present in the
system and/or pressure coupling is enabled via the Pressure Coupling Keys in the .in file. If no moldescriptor file is
provided, the element symbol (as given by the Restart File) will be printed to the output files instead of the
atom type name. In case of a pure QM calculation the charge of the moltype, the atom_type_index as well as the point_charge can be
set to 0 and the global_vdW_type can be omitted. For MM calculations that utilize just the GUFF File, the
point_charge can be set to 0 and the global_vdW_type can be omitted.
GUFF File
Default Name: guff.dat
The grand unified force field (GUFF) file can be used to define the non-bonding force field parameters for the MM atoms in the system. The GUFF file defines the Coulomb potential VCoulomb via equation (1) and the non-Coulombic potential Vnon-Coulomb via the generalized equation (2) for every atom type index in every moltype of the system in the following format:
moltype_1; atom_type_index_1; moltype_2; atom_type_index_2; rcut; c0; c1; c2; c3; c4; c5; c6; c7; c8; c9; c10; c11; c12; c13; c14; c15; c16; c17; c18; c19; c20; c21; c22(1)\[V_{\text{Coulomb}} = \frac{c_0}{r}\](2)\[V_{\text{non-Coulomb}} = \frac{c_1}{r^{c_2}} + \frac{c_3}{r^{c_4}} + \frac{c_5}{r^{c_6}} + \frac{c_7}{r^{c_8}} + \frac{c_9}{1 + e^{c_{10} (r - c_{11})}} + \frac{c_{12}}{1 + e^{c_{13} (r - c_{14})}} + c_{15} e^{c_{16} (r - c_{17})^{c_{18}}} + c_{19} e^{c_{20} (r - c_{21})^{c_{22}}}\]
The moltype and atom_type_index are defined as in the Moldescriptor file. Utilizing equation (2), Lennard-Jones, Buckingham and Morse potentials, as well as arbitrary combinations of them can be used for the description of the non-Coulombic interactions. The parameter rcut gives the cutoff radius for the non-bonded interactions. Distances are given in Å and energies in kcal/mol. The units of the parameters are chosen accordingly.
Attention
All entries in the GUFF file need to be separated via a semicolon ;. Furthermore, defining all possible interactions is mandatory. If a certain
potential is not needed, the corresponding coefficients are set to 0.
Using the GUFF file requires the Moldescriptor setup file to be provided as well.