#============================================================#
#          test rigid body simulation of a helix             #
#                                                            #
# 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[766-813]
domain helix backbone color = [ 0.6 0.6 0.6 ]  width = 2 show

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


# add ground body and joint
#--------------------------
body create  name = ground  type = ground

joint create  name = groundJnt  type = weld  domain = kcSc1 res = C[767] use = NH1
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 = [ 2 2 0 ]     \
              scale = 1.0

simulation rsim add force = force1     \
                    body = kcScBody47   \
                    time = { 0 1000 }


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

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

domain kcSc1  define region = kcSc1Rgn   residues = C[767]  atom_names = { CA }
domain kcSc47 define region = kcSc47Rgn  residues = C[813]  atom_names = { CA }

body kcScBody1 add potential = spring1       \
                  type = entropic-spring         \
                  function = graph               \
                  graph_data = { 8.0  5.0  20.2 10.0  20.5 50 }  \
                  region = kcSc1Rgn              \
                  geometry = points              \
                  color = [ 1 0.8 0 ]              \
                  width = 3              \
                  show = true

body kcScBody47 add potential = spring2          \
                  type = entropic-spring         \
                  function = graph               \
                  graph_data = { 8.0  5.0  20.2 10.0  20.5 50 }  \
                  region = kcSc47Rgn             \
                  geometry = points              \
                  show = true

simulation rsim add interaction = hspring1                   \
                    body1 = kcScBody1  potential1 = spring1  \
                    body2 = kcScBody47 potential2 = spring2  \
                    time = { 0.0 1000.0 }


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.005
simulation rsim momentum = on
#simulation  state  save_frequency = 10

#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 = [ 0.426082 0.721974 0.604492 ]
graphics  background  color = [ 1 1 1]