#============================================================#
#          test rigid body simulation of a iq12.             #
#                                                            #
# define rigid bodies for iq1 and iq2.                       #
#                                                            #
# connect bodies using a ball joint.                         #
#============================================================#

system echo = off
system verbose = false

variable width = 2.0


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


# open pdb file
#--------------
database open name = db1  format = pdb  file = ../data/neck_xform.pdb 


# read molecule
#--------------
molecule read  name = m1   database = db1
#molecule m1  xform  rotation = [ -90 0 40 ]  
molecule m1  xform  rotation = [ -50 -30 0 ]  


# create iq-cam domains
#----------------------
domain create iq1 = C[766-788]A
#domain create iq1 = C[780-788]
domain iq1 backbone color = [ 0.7 0 0 ]  width = ${width} show
#domain iq1 bonds atoms = true atom_color = [ 1 0 0 ] bond_color = [ 1 0 0 ] show

domain create iq2 = C[788-813]B
#domain create iq2 = C[788-799]
domain iq2 backbone color = [ 0 0.7 0 ]  width = ${width} show
#domain iq2 bonds atoms = true atom_color = [ 0 1 0 ] bond_color = [ 0 1 0 ] show


# create bodies
#--------------
body create  name = ground  type = ground
body create  name = iq1b  type = rigid  domain = iq1
body create  name = iq2b  type = rigid  domain = iq2

# create joints 
#--------------
joint create  name = groundJnt  type = weld  domain = iq1  res = C[780] use = CA 
joint groundJnt color = [ 1 1 1 ] msize = 0.01 shading = color show = true
joint groundJnt bodies = { ground iq1b }

joint create  name = iq12Jnt  type = ball  domain = iq1  res = C[788] use = CA 
joint iq12Jnt color = [ 1 1 0 ] msize = 0.08 shading = flat  show = true
joint iq12Jnt bodies = { iq1b iq2b }


# create a rigid simulation  
#--------------------------
simulation create name = rsim  type = rigid
simulation rsim add bodies = all
simulation rsim add joints = all

#simulation rsim print  joints = true
#simulation rsim print bodies = true 


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


# add forces
#-----------
force create  name = force1  type = explicit  global_frame = true  \
              point = iq2:C[799]  direction = [ 40 0 0 ]  scale = 1.0

simulation rsim add force = force1  body = iq2b  time = { 0 1000 }


# add spring potentials 
#-----------------------
simulation rsim  add interactions = iq1Iq2Springs   \
                 type = spring                      \
                 force_const = 50.0                 \
                 cutoff = 0.7                       \
                 use_ca = true                      \
                 time = { 0.0 1000.0 }              \
                 color = [ 0 0 0 ]                  \
                 width = 1                          \
                 show = true                        \
                 bodies = { iq1b iq2b }


#domain iq1 define region = iq1Rgn1  residues = C[780-788]  use_sidechains = true
#domain iq2 define region = iq2Rgn1  residues = C[788-799]  use_sidechains = true

#body iq1b add potential = iq1HPot1  type = spring  region = iq1Rgn1    \
          geometry = points   color = [ 0.6 0.6 0.6 ]   force_const = 10.0    \
          width = 3.0                        \
          cutoff = 0.8   show = true

#body iq2b add potential = iq2HPot1  type = spring  region = iq2Rgn1    \
          geometry = points   color = [ 1 0.6 0.6 ]   force_const = 10.0    \
          width = 3.0                        \
          cutoff = 0.8   show = true


#simulation rsim add interaction = iq1Iq2HPot             \
                    body1 = iq1b   potential1 = iq1HPot1 \
                    body2 = iq2b   potential2 = iq2HPot1 \
                    time = { 0.0 1000.0 }


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


# add trace 
#----------
simulation rsim  add trace  name = trace1  \
           global_frame = true             \
           point = iq2:C[811]              \
           body = iq2b                     \
           color = [ 1 0 1 ]   show = true 


# print body masses        
#------------------
#body  iq1b  print  properties = mass
#body  iq2b  print  properties = mass


# print interactions       
#-------------------
#simulation  rsim  interactions  print = true


simulation  rsim  write  energy = true  file_name = rsim


#graphics  center  point = [ 3.09952 4.47314 4.79906 ]
graphics  background  color = [ 1 1 1 ] 
graphics  scale = 2.0