ch3group.lt
ceb4da003907lammm-master-deprecated

ch3group.lt
View Options


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


			CH3 inherits Alkanes {

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

			write("Data Atoms") {
			$atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000
			$atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046
			$atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046
			$atom:H3 $mol:... @atom:h1 0.00 -0.8924307629540046 -0.6310438442242609 0.00
			}

			# 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 CH3 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
			$bond:b3 @bond:CH $atom:C $atom:H3
			}

			} # CH3




			######### (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