md2011-09-note_Part_2

md2011-09-note_Part_2 - O UT- OF- PLANE B ENDING I...

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Unformatted text preview: O UT- OF- PLANE B ENDING I NTERACTIONS I Out-of-plane interactions are closely related to the torsional terms I For four atoms (A,B,C,D) which for three angles (A-B-C, A-B-D, C-B-D), 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 ON-B ONDING I NTERACTION I Non-bonded 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 dipole-dipole 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...
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md2011-09-note_Part_2 - O UT- OF- PLANE B ENDING I...

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