Hello LAMMPS users,
I have a general MD question not specifically related LAMMPS. When you are defining the intramolecular terms in a force-field definition, is there a rule for the total number of intramolecular terms that should exist for a given molecule? For instance, if a molecule has 10 atoms, then it has 30 degrees of freedom (x,y,z for each atom). Is it possible to relate the number of bond, angle, dihedral, and improper terms to the number of degrees of freedom or are those terms solely dependent on the molecular structure?
Thanks,
Tim
hi tim
it depends on the type of intramolecular term in the force-field definition. if the terms are such that the bond lengths or angles are flexible (e.g. harmonic potential terms), then, as far as i know, there is no limit to the number of such terms in the force-field definition.
however, if the intramolecular terms are rigid constraints, such as those applied by the SHAKE algorithm, then there is a limit to the number of such constraints, namely the total number of degrees of freedom in the molecule (3N in three dimensions, where N is the number of atoms in the molecule). of course, if you applied 3N constraints, your molecule wouldn’t be able to move at all.
for the simple case of a non-flexible water molecule, for which the total number of degrees of freedom is 3*3 = 9, 2 bond length constraints and 1 bond angle constraint are applied (or, equivalently, 3 bond length constraints - 2 “real” bonds and 1 “artificial” bond between the hydrogen atoms), leaving the molecule with 6 degrees of freedom. These 6 degrees of freedom correspond to the 3 translational and 3 rotational degrees of freedom of the molecule as a whole. in general, for a non-linear molecule, the maximum total number of rigid constraints that can be applied (so that the molecule can still rotate and translate) is 3N-6. for a linear molecule, it is 3N-5.
-david