#============================================================#
#                  test torsion spring potential             #
#============================================================#
system echo = off
system verbose = false

# 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 = iq2Body  type = rigid   domain = iq2
body create  name = iq3Body  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 iq2Body }

joint create  name = jnt1  type = ball  domain = hc  res = C[814]  use = CA
joint jnt1 bodies = { iq2Body iq3Body }
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 = iq2Body
simulation rsim add body = iq3Body

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


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


# add forces
#-----------
force create name = force1            \
             type = explicit          \
             global_frame = true      \
             point = iq3:D[69]:CA      \
             direction = [ 0 0 10 ]   \
             scale = 1.0

simulation rsim add force = force1   \
                    body = iq3Body   \
                    time = { 0 100 }


# add torsion spring
#-------------------
body iq2Body add potential = iq2Iq3Pot1  type = torsion     \
              origin = iq2:C[814]:CA                        \
              point1 = iq2:C[806]:CA                        \
              point2 = iq2:B[69]:CA                         \
              color = [ 0.6 0.6 0.6 ]   force_const = 100.0 \
              width = 2.0  show = true  

body iq3Body add potential = iq2Iq3Pot2  type = torsion \ 
          point1 = iq3:C[824]:CA                        \
          point2 = iq3:D[69]:CA                         \
          color = [ 1 0.6 0.6 ]   force_const = 100.0   \
          width = 2.0   show = false

simulation rsim add interaction = helix1Helix2Int \
                    body1 = iq2Body  potential1 = iq2Iq3Pot1 \
                    body2 = iq3Body  potential2 = iq2Iq3Pot2 \
                    time = { 0 10000 }


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

#----------------------------
# output simulation results |
#----------------------------
simulation  rsim  write  file_name = rsim
simulation  rsim  write  energy = true  file_name = rsim
#simulation  rsim  interactions  print = true

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