#============================================================#
# test axis potential                                        #
#                                                            #
#============================================================#
system echo = off
system verbose = false

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

# read molecule
#--------------
database open name =  neck_xform  format = pdb file =  ../data/neck_xform.pdb
molecule read  database =  neck_xform  name = m1  model = 1  type = protein

# create domains
#---------------
domain create hc = C

#domain create iq2 = C[788-814]
domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0.7 0 0 ] width = 2 show
#domain iq2 pca  show=true 

#domain create iq3 = C[814-836]
domain create iq3 = DC[814-836]
domain iq3 xform  rotate = [ 0 0 45] 
domain iq3 backbone color = [ 0 0.7 0 ] width = 2 show
#domain iq3 pca  show=true 


# create bodies 
#--------------
body create  name = ground   type = ground
body create  name = iq2Body  type = rigid   domain = iq2
body create  name = iq3Body  type = rigid   domain = iq3


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

# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = iq2Body
simulation rsim add body = iq3Body

body iq2Body damping = 1.0
body iq3Body damping = 1.0


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


# add axis potential
#-------------------
#domain iq2 define region = iq2Rgn  residues = C 
domain iq2 define region = iq2Rgn  residues = BC 

#domain iq3 define region = iq3Rgn  residues = C
domain iq3 define region = iq3Rgn  residues = DC

body iq2Body add potential = iq2Axis1               \
      type = axis region = iq2Rgn  geometry = lines \
      axes = { 1 3 }  force_consts = { 1 1 1 }      \
      color = [ 1 0.6 0.6 ]  show = true 

body iq3Body add potential = iq3Axis1               \
      type = axis region = iq3Rgn  geometry = lines \
      axes = { 1 2 }                                \
      color = [ 0.6 1 0.6 ]  show = true 

simulation rsim add interaction = hspring1             \
                body1 = iq2Body  potential1 = iq2Axis1 \
                body2 = iq3Body  potential2 = iq3Axis1 \
                time = { 0.0 1000.0 }


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.01
simulation rsim momentum = on
simulation rsim damping = on
#simulation  state  save_frequency = 10


graphics center point = [ 3.77781 5.96775 3.98927 ] 


s 10000