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nbody_Dihedrals.py
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Thu, Aug 15, 05:04

nbody_Dihedrals.py
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from nbody_graph_search import Ugraph
# This file defines how dihedral interactions are generated by moltemplate.sh
# by default. It can be overridden by supplying your own custom file.
# To find 4-body "dihedral" interactions, we would use this subgraph:
#
# 1st bond connects atoms 0 and 1
# *---*---*---* => 2nd bond connects atoms 1 and 2
# 0 1 2 3 3rd bond connects atoms 2 and 3
#
bond_pattern = Ugraph([(0,1), (1,2), (2,3)])
# (Ugraph atom indices begin at 0, not 1)
def canonical_order(match):
"""
Before defining a new interaction, we must check to see if an
interaction between these same 4 atoms has already been created
(perhaps listed in a different, but equivalent order).
If we don't check for this this, we will create many unnecessary redundant
interactions (which can slow down he simulation).
To avoid this, I define a "canonical_order" function which sorts the atoms
and bonds in a way which is consistent with the symmetry of the interaction
being generated... Later the re-ordered list of atom and bond ids will be
tested against the list of atom/bond ids in the matches-found-so-far,
before it is added to the list of interactions found so far. Note that
the energy of a dihedral interaction is a function of the dihedral-angle.
The dihedral-angle is usually defined as the angle between planes formed
by atoms 0,1,2 & 1,2,3. This angle does not change when reversing the
order of the atoms. So it does not make sense to define a separate
dihedral interaction between atoms 0,1,2,3 AS WELL AS between 3,2,1,0.
So we sort the atoms so that the first atom has a lower atomID than the
last atom. (Later we will check to see if we have already defined an
interaction between these 4 atoms. If not then we create a new one.)
"""
# match[0][0:3] contains the ID numbers of the 4 atoms in the match
atom0 = match[0][0]
atom1 = match[0][1]
atom2 = match[0][2]
atom3 = match[0][3]
# match[1][0:2] contains the ID numbers of the the 3 bonds
bond0 = match[1][0]
bond1 = match[1][1]
bond2 = match[1][2]
if atom0 < atom3:
#return ((atom0, atom1, atom2, atom3), (bond0, bond1, bond2)) same as:
return match
else:
return ((atom3, atom2, atom1, atom0), (bond2, bond1, bond0))

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