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md2011-09-note_Part_2

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

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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 πε 0 q 1 q 2 r ij (6)
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I Also a dipole-dipole interaction can be implemented to act between polar groups I A functional form is (MM2): U e = μ i μ j ε 0 r 3 ij { cos χ - 3 cos α i cos α j } (7) The μ i , j are dipole moments, χ is the angle between them. The α i , j
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