#============================================================*
#                test universal joints                       *
#============================================================*

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

# read molecule 
#--------------
database open name = neck   format = pdb  file = neck_xform.pdb
molecule read  name = protein  database = neck
molecule protein xform rotation = [ -20 -40 20  ] 
domain create hc = C

# create domains
#---------------
#domain create iq1 = AC[760-788]
#domain iq1 backbone color = [ 0.7 0 0 ] width = 3 show
#domain iq1 atoms color = [ 0.7 0 0 ] show

domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0.7 0 0 ] width = 3 show
#domain iq2 atoms color = [ 0.7 0 0 ] display = point show

domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0.7 0 ] width = 3 show
#domain iq3 atoms color = [ 0 0.7 0 ] show


# create bodies from domains
#---------------------------
body create  name = ground    type = ground
body create  name = iq1_body  type = rigid   domain = iq2
body create  name = iq2_body  type = rigid   domain = iq3

# 1st joint 
# ---------
#joint create  name = jnt1   type = hinge domain = hc  res = C814  use = CA \
              use_pca = true pca_res = C[788-814]  axis1 = pca2  

#joint create  name = jnt1           \
              type = universal      \
              domain = hc           \
              res = C[814]          \
              use = CA              \
              use_pca = true        \
              pca_res = C[7880-814]  \
              axis1 = pca2          \
              axis2 = pca3

joint create  name = jnt1   type = ball domain = hc    res = C[814]     use = CA  \
              use_pca = true  pca_res = C[788-814]  axis1 = pca1  axis2 = pca2  \
              axis3 = pca3 force_const1 = 1.0  force_const2 = 2.0 force_const3 = 2.0


joint jnt1 bodies = { ground iq1_body }
joint jnt1 color = [ 1 0 1 ] msize = 0.1 shading = color show = true 


#----------------------------#
# create a rigid simulation  #
#----------------------------#

simulation create name = rsim  type = rigid

# add bodies
#-----------
simulation rsim add bodies = { ground  iq1_body iq2_body }

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

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

# add forces
#-----------
force create name = force1  type = explicit point = [ 0 0 0 ] direction = [ 1 0 0 ]  
simulation rsim add force = force1 body = iq2_body  time = { 0 1 }

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

# step simulation
#----------------
#simulation rsim step = 200


graphics background color = [ 1 1 1 ]