#============================================================*
#              test output simulated strucutres              *
#============================================================*

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


# open pdb file
#--------------
database open name =  neck_xform  format = pdb file =  ../data/neck_xform.pdb


# read molecule
#--------------
molecule read  database =  neck_xform  name = m1  model = 1  type = protein


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

domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0.7 0 0 ] width = 2 show
domain create iq2h = C[788-814]
#domain iq2h bonds  atoms = true bond_color = [ 0.7 0 0 ] atom_color = [ 0.7 0 0 ] show

domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0.7 0 ] width = 2 show
#domain iq3 atoms color = [ 0 0 1 ] render = line show

domain create iq3h = C[814-836]
#domain iq3h bonds  atoms = true bond_color = [ 0 0.7 0 ] atom_color = [ 0 0.7 0 ] show

#domain create camb = B
#domain camb  bonds  atoms = true bond_color = [ 0.7 0 0 ] atom_color = [ 1 0 0 ] show
#domain create camc = C
#domain camc  bonds  atoms = true bond_color = [ 0 0.7 0 ] atom_color = [ 0 1 0 ] show


# create bodies   
#--------------
# 1st group
body create  name = ground    type = ground
body create  name = iq2_body  type = rigid   domain = iq2
body create  name = iq3_body  type = rigid   domain = iq3


#  create joints  
#---------------
joint create  name = ground_jnt  type = weld  domain = hc    res = C[788]     use = CA \
joint ground_jnt bodies = { ground iq2_body }

joint create  name = jnt1  type = ball  domain = hc  res = C[814]  use = CA
joint jnt1 bodies = { iq2_body iq3_body }
joint jnt1 color = [ 0 0 1 ] msize = 0.04 shading = color show = true 


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


# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = iq2_body
simulation rsim add body = iq3_body


# add joints
#-----------
simulation rsim add joint = ground_jnt
simulation rsim add joint = jnt1


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


# add forces
#-----------
force create name = force1           \
             type = explicit         \
             global_frame = true     \
             point = hc:C[836]       \
             direction = [ 2 0 0 ]   \
             scale = 1.0

simulation rsim add force = force1    \
                    body = iq3_body   \
                    time = { 0 10000 }


# add interaction potentials
#---------------------------

domain iq2 define region = iq2_rgn  residues = B[102-113] 
domain iq2 define region = iq2_hrgn residues = C[809-813] 
#domain iq3 define region = iq3_hrgn residues = C[814-818]D[90-97] 
domain iq3 define region = iq3_hrgn residues = C[814-818] 

body iq2_body add potential = iq2_spring_h       \
                  type = spring                  \
                  region = iq2_hrgn              \
                  geometry = points              \
                  cutoff = 0.2                   \
                  force_const = 1.0              \
                  show = true

body iq3_body add potential = iq3_spring_h       \
                  type = spring                  \
                  region = iq3_hrgn              \
                  geometry = points              \
                  cutoff = 0.2                   \
                  force_const = 1.0              \
                  show = true

simulation rsim add interaction = hspring1                       \
                    body1 = iq2_body  potential1 = iq2_spring_h  \
                    body2 = iq3_body  potential2 = iq3_spring_h  \
                    time = { 0.0 1000.0 }


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.005
simulation rsim momentum = on
simulation  state  save_frequency = 50


# output simulation results
#--------------------------
#simulation  rsim  write  state = true  file_name = rsim
#simulation  rsim  write  domains = true  file_name = rsim 


#graphics background  color = [ 1 1 1 ]
graphics center point = [ 3.77781 5.96775 3.98927 ]