#============================================================*
#                  test random forces                        *
#============================================================*

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

# open pdb file
database open name =  neck_xform  format = pdb file =  ../data/neck_xform.pdb

# read molecule
molecule read  database =  neck_xform  name = m1  model = 1  type = protein

# create domains
domain create hc = C
domain hc  backbone  color = [ 0.6 0.6 0.6 ] width = 2 show
domain create iq1 = AC[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show
domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show
domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 2 show

#--------------------------------------------------------------#
#                      create bodies                           #
#--------------------------------------------------------------#
body create  name = ground    type = ground
body create  name = iq1_body  type = rigid   domain = iq1
body create  name = iq2_body  type = rigid   domain = iq2
body create  name = iq3_body  type = rigid   domain = iq3


#--------------------------------------------------------------#
#                      create joints                           #
#--------------------------------------------------------------#
# 1st group
joint create  name = jnt1   type = ball    domain = hc    res = C[760]     use = CA
joint jnt1 bodies = { ground iq1_body }
joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 

joint create  name = jnt2   type = ball    domain = hc    res = C[788]     use = CA
joint jnt2 bodies = { iq1_body iq2_body }
joint jnt2 color = [ 0 1 0 ] msize = 0.1 shading = color show = true

joint create  name = jnt3   type = ball    domain = hc    res = C[814]     use = CA
joint jnt3 bodies = { iq2_body iq3_body }
joint jnt3 color = [ 0 0 1 ] msize = 0.1 shading = color show = true 

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

simulation create name = rsim  type = rigid

# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = iq1_body
simulation rsim add body = iq2_body
simulation rsim add body = iq3_body

# add joints
#-----------
simulation rsim add joint = jnt1
simulation rsim add joint = jnt2
simulation rsim add joint = jnt3


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


# add forces
#-----------
force create name = force1        \
             type = random        \
             mean = 0.0           \
             sd = 1000.0           \
             seed = 147321        \
             scale = 0.1

simulation rsim add force = force1    \
                    body = iq3_body   \
                    time = { 0 1000 }


# add interaction potentials
#---------------------------
#read pot.pmc


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim momentum = off


# step simulation
#----------------
#simulation rsim step = 200