#============================================================*
#               test simulation using ball joints            *
#                                                            *
# 8 bodies with 1 residue each.                              *
#============================================================*

# set units
units
units scale  name = mass   uname = reducedMass   value = 10000.0

# open pdb file
database open name = neck format = pdb  file = neck_xform.pdb

# read molecule
molecule read  name = m1   database = neck
#molecule m1  xform  translation = [ -1.9540  -8.7018  -4.8071 ] 

# create a some domains
domain create iq = C[760-788]
#domain iq backbone color = [ 0.6 0.6 0.6 ] width = 2 show
#domain iq bonds bond_color = [ 1 1 1 ] width = 2 show

domain create r1 = C760
#domain create r1 = C[760-761]
#domain r1 atoms color = [ 1 0 0 ] show
#domain r1 bonds atoms = true  atom_color = [ 1 0 0 ]  bond_color = [ 1 0 0 ]  show
domain r1 bonds atoms = true  atom_color = element  bond_color = [ 1 0 0 ]  show

domain create r2 = C761
#domain r2 atoms color = [ 0 1 0 ] show
#domain r2 bonds atoms = true  atom_color = [ 0 1 0 ] bond_color = [ 0 1 0 ] show
domain r2 bonds atoms = true  atom_color = element bond_color = [ 0 1 0 ] show

domain create r3 = C762
#domain r3 atoms color = [ 1 1 0 ] show
domain r3 bonds atoms = true  atom_color = element bond_color = [ 1 1 0 ] width = 2 show

domain create r4 = C763
#domain r4 atoms color = [ 0 1 1 ] show
domain r4 bonds atoms = true  atom_color = element bond_color = [ 0 1 1 ] width = 2 show

domain create r5 = C764
#domain r5 atoms color = [ 1 0 0 ] show
domain r5 bonds atoms = true  atom_color = element bond_color = [ 0 1 1 ] width = 2 show

domain create r6 = C765
#domain r6 atoms color = [ 0 1 0 ] show
domain r6 bonds atoms = true  atom_color = element bond_color = [ 0 1 0 ] width = 2 show

domain create r7 = C766
#domain r7 atoms color = [ 1 1 0 ] show
domain r7 bonds atoms = true  atom_color = element bond_color = [ 1 1 0 ] width = 2 show

domain create r8 = C767
#domain r8 atoms color = [ 0 1 1 ] show
domain r8 bonds atoms = true  atom_color = element bond_color = [ 0 1 1 ] width = 2 show

body create  name = ground    type = ground
body create  name = r1b  type = rigid   domain = r1
body create  name = r2b  type = rigid   domain = r2
body create  name = r3b  type = rigid   domain = r3
body create  name = r4b  type = rigid   domain = r4
body create  name = r5b  type = rigid   domain = r5
body create  name = r6b  type = rigid   domain = r6
body create  name = r7b  type = rigid   domain = r7
body create  name = r8b  type = rigid   domain = r8

joint create  name = jnt1   type = ball  domain = iq res = C760   use = CA
joint jnt1 color = [ 1 0 0 ] msize = 0.02 shading = color show = true
joint jnt1 bodies = { ground r1b }

joint create  name = jnt2   type = ball  domain = iq res = C761   use = CA
joint jnt2 color = [ 0 1 0 ] msize = 0.02 shading = color show = true
joint jnt2 bodies = { r1b r2b }

joint create  name = jnt3   type = ball  domain = iq res = C762   use = CA
joint jnt3 color = [ 1 1 0 ] msize = 0.02 shading = color show = true
joint jnt3 bodies = { r2b r3b }

joint create  name = jnt4   type = ball  domain = iq res = C763   use = CA
joint jnt4 color = [ 1 0 1 ] msize = 0.02 shading = color show = true
joint jnt4 bodies = { r3b r4b }

joint create  name = jnt5   type = ball  domain = iq res = C764   use = CA
joint jnt5 color = [ 1 0 1 ] msize = 0.02 shading = color show = true
joint jnt5 bodies = { r4b r5b }

joint create  name = jnt6   type = ball  domain = iq res = C765   use = CA
joint jnt6 color = [ 1 0 1 ] msize = 0.02 shading = color show = true
joint jnt6 bodies = { r5b r6b }

joint create  name = jnt7   type = ball  domain = iq res = C766   use = CA
joint jnt7 color = [ 1 0 1 ] msize = 0.02 shading = color show = true
joint jnt7 bodies = { r6b r7b }

joint create  name = jnt8   type = ball  domain = iq res = C767   use = CA
joint jnt8 color = [ 1 0 1 ] msize = 0.02 shading = color show = true
joint jnt8 bodies = { r7b r8b }


# create a rigid simulation
#--------------------------
simulation create name = rsim  type = rigid


# add bodies
#-----------
simulation rsim add bodies = { ground r1b r2b r3b r4b r5b r6b r7b r8b }

# add joints
#-----------
simulation rsim add joints = { jnt1 jnt2 jnt3 jnt4 jnt5 jnt6 jnt7 jnt8 }

# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on

# add forces
#-----------
force create  name = force1         \
              type = explicit         \
              global_frame = true             \
              point = [ -.2384   0.1716   0.3084 ]    \
              direction = [ 0.5 0 0 ]  \
              scale = 1.0

simulation rsim add force = force1    \
                    body = r2b   \
                    time = { 0 1000 }


# initialize simulation
#----------------------
simulation rsim initialize

graphics center point = [ 0 0 0 ]