#============================================================#
# define rigid bodies for peptide plane and sidechains.      #
#                                                            #
# use multibody command.                                     #
#============================================================#

system echo = off
system verbose = false

# 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

# create helix domain
#--------------------
domain create helix = C[783-789]
domain helix backbone planes color = [ 1 1 1 ]  width = 3 show

#--------------------------------------------------------------#
#                 create kinematic chain                       #
#--------------------------------------------------------------#
multibody  create  name = kc  domain = helix  type = kinematic_chain

# add ground joint
#-----------------

body create  name = ground  type = ground

#joint create  name = groundJnt  type = weld  domain = kcSc1 res = C[783] use = CA
#joint groundJnt color = [ 1 1 1 ] msize = 0.01 shading = color show = true
#joint groundJnt bodies = { ground kcScBody1 }


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


# add forces
#-----------
force create  name = force1             \
              type = explicit           \
              point = [ 0 0 0 ]         \
              global_frame = false      \
              direction = [ 1 0 0 ]     \
              scale = 1.0

simulation rsim add force = force1     \
                    body = kcScBody6   \
                    time = { 0 1000 }


#--------------------------------------------------------------#
#                 add spring potentials                        #
#--------------------------------------------------------------#

# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.01
#simulation rsim momentum = on
#simulation  state  save_frequency = 100

#simulation rsim  add trace  name = trace1  color = [ 1 0 1 ]  \
           global_frame = true    \
           point = kcSc76:C[836]  \
           body = kcScBody76   show = true

#----------------------------
# print body masses         |
#----------------------------
#body  d1b  print  properties = mass
#body  d2b  print  properties = mass


graphics  center  point = [ 1.32939 2.57201 2.19204 ]