#============================================================*
#               test simulation of peptide planes            *
#                                                            *
# use pin joints.                                            *
#============================================================*

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

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

database open name = db1  format = pdb  file = d1x.pdb
molecule read  name = m1   database = db1
domain create d1 = A
domain d1 bonds  atoms = true  atom_color = [ 1 0 0 ] \
                 render = line \
                 bond_color = [ 1 0 0 ] width = 3 show

database open name = db2  format = pdb  file = d2x.pdb
molecule read  name = m2   database = db2
domain create d2 = A
domain d2 bonds  atoms = true  atom_color = [ 0 1 0 ] \
                 bond_color = [ 0 1 0 ] width = 3 show

database open name = db3  format = pdb  file = d3x.pdb
molecule read  name = m3   database = db3
domain create d3 = A
domain d3 bonds  atoms = true  atom_color = [ 0 1 1 ] \
                 render = line \
                 bond_color = [ 0 1 1 ] width = 3 show


#--------------------------------------------------------------#
#                      create bodies                           #
#--------------------------------------------------------------#
body create  name = d1b  type = rigid   domain = d1
body create  name = d2b  type = rigid   domain = d2
body create  name = d3b  type = rigid   domain = d3
body create  name = ground type = ground  

#--------------------------------------------------------------#
#                      create joints                           #
#--------------------------------------------------------------#

joint create  name = jnt1  type = pin domain = d2  res = A3 use = N \
              use_bond = true   bond = { d1:A3:N d2:A3:CA }
joint jnt1 color = [ 0 1 0 ] msize = 0.02 shading = color show = true
joint jnt1 bodies = { d1b d2b }

joint create  name = jnt2  type = pin domain = d2  res = A3 use = C \
              use_bond = true   bond = { d2:A3:CA d3:A3:C }
joint jnt2 color = [ 0 1 0 ] msize = 0.02 shading = color show = true
joint jnt2 bodies = { d2b d3b }

joint create  name = jntg  type = ball domain = d2  res = A3  use = OE1
joint jntg color = [ 0 1 0 ] msize = 0.01 shading = color show = true
joint jntg bodies = { ground d1b }


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

simulation create name = rsim  type = rigid
simulation rsim solver = ode
simulation rsim solver finite_rotation = on


# add bodies
#-----------
simulation rsim add bodies = { ground d1b d2b d3b }

# add joints
#-----------
simulation rsim add joints = { jnt1 jnt2 jntg }

# add forces
#-----------
force create  name = force1                           \
              type = explicit                         \
              global_frame = true                     \
              point = [ 0.2499 0.162477 0.284767 ]    \
              direction = [  -0.2  0 0 ]              \
              scale = 1.0

simulation rsim add force = force1    \
                    body = d2b        \
                    time = { 0 1000 }


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


#graphics center point = [ 0 0 0 ]