#============================================================*
#               test simulation using ball joints            *
#                                                            *
# two bodies with 4 residues 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[760-780]
domain iq backbone color = [ 0.6 0.6 0.6 ] width = 1 show
#domain iq bonds bond_color = [ 1 1 1 ] width = 2 show

domain create r1 = C[760-764]
#domain r1 atoms color = [ 1 0 0 ] display = line show
#domain r1 bonds atoms = false atom_color = element bond_color = [ 1 0 0 ] width = 2 show
domain r1 bonds atoms = true  atom_color = element bond_color = [ 1 0 0 ] width = 2 show
#domain r1 backbone color = [ 1 0 0 ] width = 3 show

domain create r2 = C[764-768]
#domain r2 atoms color = [ 0 1 0 ] show
#domain r2 bonds atoms = false atom_color = element bond_color = [ 0 1 0 ] width = 2 show
domain r2 bonds atoms = true  atom_color = element bond_color = [ 0 1 0 ] width = 2 show
#domain r2 backbone color = [ 0 1 0 ] width = 3 show

body create  name = ground    type = ground
body create  name = r1b  type = rigid   domain = r1
body create  name = r2b  type = rigid   domain = r2

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 = C764   use = CA
joint jnt2 color = [ 0 1 0 ] msize = 0.02 shading = color show = true
joint jnt2 bodies = { r1b r2b }

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


# add bodies
#-----------
simulation rsim add bodies = { ground r1b r2b }

# add joints
#-----------
simulation rsim add joints = { jnt1 jnt2 }

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

# add forces
#-----------
force create  name = force1         \
              type = explicit         \
              global_frame = true             \
              point = [ 0.956219 0.85662 0.291279 ]    \
              direction = [ .1 0 0 ]  \
              scale = 1.0

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


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

simulation rsim time step = 0.001 


graphics center  point = [ 0 0 0 ]