Developers.ForceFields.inter

Guide on intermolecular force fields in MolDynSim

The intermolecular force field describes the interaction between two molecules (of equal or different chemical species). Typically, these force fields are expressed in terms of distances between pairs of atoms. However, you can feel free to implement also radically different forms of force fields for use in your simulations using MolDynSim.

Examples

• LJ_12_6 potential for rare gases where the force field is expressed in terms of repulsive (R-12) and attractive (R-6) interactions.

• TIP_3P potential for water where the force field is expressed in terms Coulomb and Lennard-Jones interactions.

• Angle-dependent(!) DIM potential for molecule-rare gas interaction where the force field is expressed in terms of the angle between the X-X bond and the vector connecting to the rare gas atom.

MATLAB coding

• Function header
  function u = myfunction (parameters,q1,q2)
• function name (here myfunction) is specified as a function handle which is a field of structured variable inter{i,j} upon MolDynSim initialization
• input q1: specifies the coordinates of all atoms within the first molecule in a 3*N1 real matrix
• input q2: specifies the coordinates of all atoms within the second molecule in a 3*N2 real matrix
• input parameters: a structure containing all parameters necessary for this choice of potential function. It is also set as a field of structured variable inter{i,j} upon MolDynSim initialization
• output u: A real number returning the energy in units of kJ/mol.