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 epsilon 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.

• no_14

  This parameter tells that all 1-4 pairs must be excluded from the intramolecular Lennard-Jones and electrostatic interactions

• noi15

  This parameter tells that all intramolecular electrostatic and LJ interactions are switched off

• sel14 <factor>

  Scale 1-4 electrostatic interactions by this factor

• slj14 <factor>

  Scale 1-4 Lennard-Jones interactions by this factor

• 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)

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.