Variable "inter{.,.}" in MolDynSim
This variable characterizes the intermolecular force fields in our simulations, i.e. for interaction between pairs of molecules of (equal and different!) species. It is used in essentially all of the MolDynSim programs. Every entry of the cell matrix is a structured variable containing the following items
Settable parameters
| field |
description |
| handle |
choice of force field to be used (MATLAB function handle); normally found in +ff2 package |
| parameter |
structure containing all necessary parameters, depending on the choice of the function handle, see below |
| @ff2.Morse |
anharmonic Morse oscillator for interaction between monatomic species |
| d_e |
dissociation energy (well depth, in kJ/mol) |
| r_e |
position of minimum (in nm) |
| alf |
range parameter (inverse length, in 1/nm) |
| @ff2.LJ_12_6 |
Lennard-Jones non-bonded interaction between non-bonded, monatomic species |
| eps |
well depth (in kJ/mol) |
| sig |
root (in nm). Note that position of minimum is 2^(1/6)*sig |
| @ff2.Coul_Buck |
Coulomb-Buckingham intermolecular potential, e.g., for ionic crystals |
| q_q |
Product of charges, in e^2 |
| bij |
Energy parameter for short range repulsion, in kJ/mol |
| rho |
Length parameter for short range repulsion, in nm |
| c_6 |
Energy parameter for dispersion attraction, in kJ/mol*nm^6 |
| @ff2.TIP_3P |
Three-particle model of water: Three Coulomb sites (on O,H,H) and one LJ-site (on O atom) |
| q |
Three charges, row vector, in e |
| a |
Energy parameter for short range repulsion, in kJ/mol*nm^12 |
| c |
Energy parameter for dispersion attraction, in kJ/mol*nm^6 |
| @ff2.TIP_4P |
Four-particle model of water: Three Coulomb sites (on H,H,dummy) and one LJ-site (on O atom) |
| q |
Four charges (first one: zero), row vector, in e |
| a |
Energy parameter for short range repulsion, in kJ/mol*nm^12 |
| c |
Energy parameter for dispersion attraction, in kJ/mol*nm^6 |
Internal variables
| field |
description |
| thaw_thaw |
table of interaction energies between thawed and thawed molecules |
| thaw_froz |
table of interaction energies between thawed and frozen molecules |
| froz_thaw |
table of interaction energies between frozen and thawed molecules |
Note that these tables are needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction between frozen molecules is disregarded.
Write your own intermolecular force field:
- If you cannot find a suitable function inside the +ff2 package, you will have to provide one yourself. For a guide how to write an intermolecular force field, please see here.
