Re. Tuzun et al., MOLECULAR-DYNAMICS TREATMENT OF TORSIONAL INTERACTIONS ACCOMPANIED BYDISSOCIATION, Macromolecular theory and simulations, 4(5), 1995, pp. 909-920
When three atoms in a bend sequence move into a linear configuration,
any torsional angle involving those three atoms becomes undefined and
its Cartesian derivatives singular. In molecular dynamics simulations,
this is most likely to occur during and after a bond-breaking process
, leading to spuriously large torsional forces and energies which inva
lidate the simulation. By including appropriate bend angle switching f
unctions in torsional interaction terms, one may approach the linear b
end limit in a well-defined manner and make torsional forces vanish ar
ound this limit, as expected on physical grounds. Although this makes
potential energy terms more complicated and force evaluations more exp
ensive, this expense can be greatly reduced by observing that any inte
rnal force must not move the center of mass of the particles involved.
Several approximations explored in this paper can reduce this effort
even further.