#============================================================*
#                  test spring potential                     *
#                                                            *
# use springs on mainchain atoms.                            *
#============================================================*

# 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                           #
#--------------------------------------------------------------#
# 1st group
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 = explicit         \
             point = [ 0 0 0 ]       \
             direction = [ 10 0 0 ]   \
             scale = 1.0

simulation rsim add force = force1    \
                    body = iq3_body   \
                    time = { 0 2 }


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

domain iq1 define region = iq1_rgn  residues = A[7-19]    atom_names = { CA C O }
domain iq2 define region = iq2_rgn  residues = B[102-113] atom_names = { CA C O }
domain iq2 define region = iq2_hrgn residues = C[809-813] atom_names = { CA C O }
domain iq3 define region = iq3_hrgn residues = C[814-818] atom_names = { CA C O }

body iq1_body add potential = iq1_spring         \
                  type = spring                  \
                  region = iq1_rgn               \ 
                  geometry = points              \
                  force_const = 5.0              \
                  cutoff = 2.0                   \
                  show = true               

body iq2_body add potential = iq2_spring         \
                  type = spring                  \
                  region = iq2_rgn               \
                  geometry = points              \
                  force_const = 2.0              \
                  show = true

body iq2_body add potential = iq2_spring_h       \
                  type = spring                  \
                  region = iq2_hrgn              \
                  geometry = points              \
                  force_const = 2.0              \
                  show = true

body iq3_body add potential = iq3_spring_h       \
                  type = spring                  \
                  region = iq3_hrgn              \
                  geometry = points              \
                  force_const = 2.0              \
                  show = true

simulation rsim add interaction = spring1                       \
                    body1 = iq1_body  potential1 = iq1_spring   \ 
                    body2 = iq2_body  potential2 = iq2_spring   \ 
                    time = { 0.0 1000.0 }

simulation rsim add interaction = hspring1                       \
                    body1 = iq2_body  potential1 = iq2_spring_h  \
                    body2 = iq3_body  potential2 = iq3_spring_h  \
                    time = { 0.0 1000.0 }


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


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