#============================================================#
#          test rigid body simulation of a helix             #
#                                                            #
# define rigid bodies for peptide plane and sidechains.      #
#============================================================#

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
#domain helix backbone color = [ 1 1 1 ]  width = 3 show


#--------------------------------------------------------------#
#                     create domains                           #
#--------------------------------------------------------------#

read doms.pmc


#--------------------------------------------------------------#
#                create cg model                               #
#--------------------------------------------------------------#

read model.pmc


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

simulation create name = rsim  type = rigid

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


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


# add forces
#-----------
force create  name = force1             \
              type = explicit           \
              point = d16:C[791]:CB     \
              global_frame = true       \
              direction = [ 0 0.1 0 ]   \
              scale = 1.0

simulation rsim add force = force1     \
                    body = d16b        \
                    time = { 0 1000 }

#--------------------------------------------------------------#
#                 add spring potential                         #
#--------------------------------------------------------------#

read pot.pmc


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.01
simulation rsim momentum = on
#simulation  state  save_frequency = 250


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


graphics  center  point = [ 1.32939 2.57201 2.19204 ]