Variable "intra{.}" in MolDynSim
This variable characterizes the intramolecular force fields for each molecular species in our simulations. It is used in essentially all of the MolDynSim programs. Every entry of the cell vector is a structured variable that containing the following items
Settable parameters
| field |
description |
| handle |
choice of force field to be used (MATLAB function handle, see below); normally found in +ff1 package |
| parameter |
structure containing all necessary parameters, depending on the choice of the function handle, see the following lists |
| @ff1.Morse |
anharmonic Morse oscillator (so far only for diatomics) |
| d_e |
dissociation energy (well depth, in kJ/mol) |
| r_e |
position of minimum (in nm) |
| alf |
range parameter (inverse length, in 1/nm) |
| @ff1.Harmonic |
harmonic force field (so far only for bent ABA triatomics, e.g., H2O) |
| r_0 |
equilibrium bond length, in nm |
| a_0 |
equilibrium bond angle, in rad |
| k_r |
stretching force constant, in kJ/(mol*nm^2) |
| k_a |
bending force constant, in kJ/(mol*rad^2) |
Internal variables
| field |
description |
| thawed |
table of interaction energies inside thawed molecules |
Note that this table is needed for efficient evaluation of gradient and Hessian of the intramolecular force field. Interaction inside frozen molecules is disregarded.
Write your own intramolecular force field:
- If you cannot find a suitable function inside the +ff1 package, you will have to provide one yourself. For a guide how to write an intramolecular force field, please see here.
