ch2group.lt
4a1807d39739lammm-master

ch2group.lt
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			import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes


			CH2 inherits Alkanes {

			# atom-id mol-id atom-type charge x y z

			write("Data Atoms") {
			$atom:C $mol:... @atom:c3 -0.120 0.000 0.000 0.000
			$atom:H1 $mol:... @atom:h1 0.060 0.000 0.63104384422426 0.892430762954
			$atom:H2 $mol:... @atom:h1 0.060 0.000 0.63104384422426 -0.892430762954
			}

			# Note: The "..." in "$mol:..." tells moltemplate that this molecule may
			# be a part of a larger molecule, and (if so) to use the larger
			# parent object's molecule id number as it's own.
			# The CH2 group is part of the Hexadecane molecule.

			# Now specify which pairs of atoms are bonded:
			# bond-id bond-type atom-id1 atom-id2

			write('Data Bonds') {
			$bond:b1 @bond:CH $atom:C $atom:H1
			$bond:b2 @bond:CH $atom:C $atom:H2
			}

			} # CH2




			# Atom charges for this example were taken from the OPLSAA force field file:
			# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
			#
			######### (scratchwork calculations for the atomic coordinates) #########
			# Lcc = 1.5350 # length of the C-C bond (Sp3)
			# Lch = 1.0930 # length of the C-H bond
			# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
			# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
			# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
			# # 0.5*DeltaYc = 0.4431163316030377
			# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
			# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609