Biomedical Engineering Reference
In-Depth Information
4.6.2 Cut-Offs
For a largemolecule, there aremanymore nonbonded interactions than bonded interactions.
Molecular mechanics force fields very often cut these off to zero at some finite distance, in
order to save computer time. This can sometimes lead to mathematical difficulties because
of the discontinuity, and various ingenious methods have been proposed to circumvent the
problem (other than actually retaining the terms). I will show you in a later chapter that
there are other problems associated with this cut-off procedure; it is a real problem, not just
one that I have mentioned out of historical interest.
Figure 4.5 shows a Lennard-Jones 12-6 potential with a cut-off (after a certain value of
R
, the potential is set to zero).
Intermolecular distance R
Figure 4.5
Schematic cut-off of Lennard-Jones potential
4.7 Modern Force Fields
A 'standard' modern MM force field can be written
U
=
U
AB
+
U
ABC
+
U
ABCD
+
U
ABCD
+
U
AB
+
U
AB
stretch
bend
dihedral
out-of -plane
nonbonded
Coulomb
(4.18)
