Optional features of the force field

Description of the optional features of the force field begins with the line defining the type of additional potential features. These are:

• tors1

  describes torsion angles in terms of MM3 potential:

    $$U_{tors}(\phi) = K_1(1+\cos{\phi})/2 + K_2(1-\cos{2\phi})/2 + K_3(1+\cos{3\phi})/2$$ (8)

  The first line of this section contains the number of torsions of this type followed by lines in which fields 1)-4) define atoms and fields 5)-7) constants $K_1,K_2$ and $K_3$ in $kJ/M$ for each torsion angle of this type.

• tors5

  describes torsion angles given by the Ryckaert-Bellemans potential:

    $$U_{tors}(\phi) = \sum_{i=1}^5 K_i\cos^i(\phi - 180)$$ (9)

  The first line of this section contains the number of torsions of this type followed by lines in which fields 1)-4) define atoms and fields 5)-9) constants $K_1,...,K_5$ in $kJ/M$ for each torsion angle of this type.

• improper

  improper dihedral potential:

    $$U_{impr}(\phi) = k_{\phi}(\phi - \phi_0)^2$$ (10)

  field 5) is the equilibrium angle in degrees and 6) is the force constant

• special

  introduces a list, over-reading Lennard-Jones parameters for 1-4 interactions for the specified atoms. This list consists of the following:

  the first line - number of atoms in the list;

  other lines: the first field defines atom, the second is $\sigma$ (Å) and the third parameter is $\varepsilon$ in $kJ/M$.

  Scaling parameter for 1-4 LJ interactions, eventually specified by slj14 keyword (see below), is applied to these modified LJ parameters also.

• sel14 <factor>

  Scale 1-4 electrostatic interactions by this factor

• slj14 <factor>

  Scale 1-4 Lennard-Jones interactions by this factor. This applies also to LJ parameters modified by keywords special or par14 of the .mmol file, and to parameters introduced by Pair_list keyword of the input file.

• par14

  Assign special LJ parameters for 1-4 neighbours

  This parameter follows by a line specifying the number of special 1-4 pairs followed by the corresponding number of lines with four parameters: site numbers of the first and second atom, then LJ parameter $\sigma$ (Å) and LJ parameter $\varepsilon$ (kJ/mol).

  Note: There are several ways to modify LJ parameters for 1-4 interactions. They are applied in the following order (each next definition overrides the previous ones):

  1. Default (Lorentz-Berthelot or those specified in the input file) combination rules are applied
  2. Special Lennard-Jones parameters for each atom (defined by the special section of the .mmol file) are applied
  3. Special 1-4 Lennard-jones parameters for atom pairs from the par14 section of the .mmol file are applied
  4. Global list of LJ interaction parameters introduced by Pair_list keyword of the input file is applied
  5. All parameters for 1-4 LJ pairs (both modified and unmodified) are scaled by the factor introduced by slj14 keyword for the corresponding molecular type

• fSPC

  This parameter is exclusively for the flexible SPC model. It tells to the program to compute water intramolecular potential according to the paper by Toukan and Rahman, Phys. Rev. B, 31(2) 2643 (1985). It is possible to change internal bond parameters in the .mmol file.

Examples of .mmol files are included into moldb directory. For big molecules, procedure of writing .mmol files may be somewhat automatized by the utility makemol.