# a simple butane molecule is being investigated.

# first define some colors
color id=0 rgb=[1.0,1.0,1.0]
color id=1 rgb=[1.0,0.0,0.0]
color id=2 rgb=[0.0,1.0,0.0]
color id=3 rgb=[0.0,0.0,1.0]
color id=4 rgb=[0.3,0.3,0.3]

# define the box
box cell=[25,25,25]

# ------------------------------------------
# the carbon chain 
scale x=1.5 y=1.5 z=1.5
particle m=21894.71 q=6.0 r=1.46 p=[0.0,0.0,0.0] x=[-4.0,0.0,0.0] c=4 id=1
particle                                       x=[-2.0,0.0,0.0] 
particle                                       x=[0.0,0.0,0.0] 
particle                                       x=[2.0,0.0,0.0] 

# the bonding forces between the carbons
interaction harmonic f=1.275 r0=2.89 { 1 2 }
interaction harmonic f=1.275 r0=2.89 { 2 3 }
interaction harmonic f=1.275 r0=2.89 { 3 4 }

# the bond bending forces between the carbons
interaction bending f=0.175 deg=112.4  { 1 2 3 4 }

# then the torsional force between the carbons
interaction torsional f=0.0175 n=1 deg=180.0 { 1 2 3 4 }


# ------------------------------------------
# now for the hydrogen atoms on C1
translate x=-4.0
scale x=2.25 y=2.25 z=2.25
particle m=1827.81 q=1.0 r=0.701 p=[0.0,0.0,0.0] x=[1.0,0.0,0.0] c=0 id=100
particle                                        x=[0.0,1.0,0.0]
particle                                        x=[0.0,0.0,1.0]

# the H-C-H bending forces of the first CH3
interaction bending  f=0.175 deg=107.7  { 100 1 101 }
interaction bending  f=0.175 deg=107.7  { 101 1 102 } 
interaction bending  f=0.175 deg=107.7  { 102 1 100 }

#the H-C-C bending forces of the first CH3
interaction bending f=0.175 deg=111.2   { 2 1 100 }
interaction bending f=0.175 deg=111.2   { 2 1 101 }
interaction bending f=0.175 deg=111.2   { 2 1 102 }

# the bonding interactions of the first CH3
interaction harmonic f=1.195 r0=3.76    { 1 100 }
interaction harmonic f=1.195 r0=3.76    { 1 101 }
interaction harmonic f=1.195 r0=3.76    { 1 102 }


# ------------------------------------------
# now for the hydrogen atoms on C2
translate x=-2.0
scale x=2.25 y=2.25 z=2.25
particle                                       x=[1.0,0.0,0.0] id=200
particle                                       x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C2
interaction bending  f=0.175 deg=106.1  { 200 2 201 }

# the four CH2 C-C-H bending on C2
interaction bending  f=0.175 deg=109.5  { 1 2 200 }
interaction bending  f=0.175 deg=109.5  { 1 2 201 }
interaction bending  f=0.175 deg=109.5  { 3 2 200 }
interaction bending  f=0.175 deg=109.5  { 3 2 201 }

# the bonding interactions of the first CH2 on C2
interaction harmonic f=1.195 r0=3.76    { 2 200 }
interaction harmonic f=1.195 r0=3.76    { 2 201 }


# ------------------------------------------
# now for the hydrogen atoms on C3
translate x=0.0
scale x=2.25 y=2.25 z=2.25
particle                                       x=[1.0,0.0,0.0] id=300
particle                                       x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C3
interaction bending  f=0.175 deg=106.1  { 300 3 301 }

# the four CH2 C-C-H bending on C3
interaction bending  f=0.175 deg=109.5  { 2 3 300 }
interaction bending  f=0.175 deg=109.5  { 2 3 301 }
interaction bending  f=0.175 deg=109.5  { 4 3 300 }
interaction bending  f=0.175 deg=109.5  { 4 3 301 }

# the bonding interactions of the second CH2 on C3
interaction harmonic f=1.195 r0=3.76    { 3 300 }
interaction harmonic f=1.195 r0=3.76    { 3 301 }


# ------------------------------------------
# now for the hydrogen atoms on C4
translate x=2.0
scale x=2.25 y=2.25 z=2.25
particle                                        x=[1.0,0.0,0.0] id=400
particle                                        x=[0.0,1.0,0.0]
particle                                        x=[0.0,0.0,1.0]

# the H-C-H bending forces of the second CH3
interaction bending  f=0.175 deg=107.7  { 400 4 401 }
interaction bending  f=0.175 deg=107.7  { 401 4 402 } 
interaction bending  f=0.175 deg=107.7  { 402 4 400 }

#the H-C-C bending forces of the second CH3
interaction bending f=0.175 deg=111.2   { 3 4 400 }
interaction bending f=0.175 deg=111.2   { 3 4 401 }
interaction bending f=0.175 deg=111.2   { 3 4 402 }

# the bonding interactions of the first CH3
interaction harmonic f=1.195 r0=3.76    { 4 400 }
interaction harmonic f=1.195 r0=3.76    { 4 401 }
interaction harmonic f=1.195 r0=3.76    { 4 402 }


# ------------------------------------------
# find stable situation first
conformation n=10000 error=1.0E-4 maxstep=2.5

# ------------------------------------------
# then setup a constant temperature
temperature k=3.166829379841521e-06 constant=293.0 tau=206.7055

# and finaly the dynamics statement, run 100 ps with steps of 0.1 fs
dynamics dt=4.13411 tend=4134110.5461 t=0.0 error=3.67493E-6