#============================================================*
#               test rigid body simulation of a loop         *
#                                                            *
# res 593-613                                                *
#                                                            *
# define domains consisting of peptide and sidechain groups. *
# use multibody command.                                     *
#============================================================*

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

# open pdb file
database open name = db1  format = pdb  file = ../data/loop_piece.pdb

# read molecule
molecule read  name = m1   database = db1


domain create loop  = C
domain loop backbone color = [ 0.6 0.6 0.6 ] width = 1 show

#domain create loop1  = C[596-600]
domain create loop1  = C[596-606]
domain loop1 backbone color = [ 0.6 0.0 0.0 ] width = 2 show

# create kinematic chain
#-----------------------
multibody  create  name = kc  domain = loop1  type = kinematic_chain

body create  name = ground    type = ground

joint create  name = groundJnt  type = ball domain = kcPt1 res = C[596] use = C
joint groundJnt color = [ 1 1 1 ] msize = 0.01 shading = color show = true
joint groundJnt bodies = { ground kcPtBody1 }

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

simulation create name = rsim  type = rigid

simulation rsim add bodies = all 
simulation rsim add joints = all 

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


# add forces
#-----------

force create  name = force2             \
              type = explicit           \
              point = kcSc10:C[606]:C   \
              global_frame = true       \
              direction = [ 0 0 0.2 ]  \
              scale = 1.0

simulation rsim add force = force2    \
                    body = kcScBody10  \
                    time = { 0 1000 }


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

simulation rsim time step = 0.001