This preview shows pages 1–3. Sign up to view the full content.
This preview has intentionally blurred sections. Sign up to view the full version.
View Full Document
Unformatted text preview: O UT OF PLANE B ENDING I NTERACTIONS I Outofplane interactions are closely related to the torsional terms I For four atoms (A,B,C,D) which for three angles (ABC, ABD, CBD), there can be an energy cost for moving one of the atoms out of the plane spanned by the three other atoms I This can be accounted for in one of two main ways: I Harmonic potential I Improper torsion term N ONB ONDING I NTERACTION I Nonbonded interactions act both between atoms in the same molecule and those in other molecules I These are often divided to I Electrostatic interactions I Van der Waals interactions I The electrostatic part arises from charge differences within a molecule I This can be modeled by distributing point charges in the molecule I Of course, the simple approach is to implement an interaction of the form (CHARMm & AMBER) U elect = 1 4 q 1 q 2 r ij (6) I Also a dipoledipole interaction can be implemented to act between polar groups I A functional form is (MM2): U e = i j r 3 ij { cos  3 cos i cos j } (7) The i , j are dipole moments, is the angle between them. The i , j are the angles between the moments...
View
Full
Document
 Winter '12
 Kotakoski

Click to edit the document details