#============================================================* # test simulation of cylinders from domain * # * # allign cylinders with previous one. * #============================================================* # set units #---------- units units scale name = mass uname = reducedMass value = 10000.0 # open pdb file #-------------- database open name = neck_xform format = pdb file = neck_xform.pdb # read molecule #-------------- molecule read database = neck_xform name = m1 model = 1 type = protein # create domains #--------------- domain create hc = C # translate domain so that ground joint will be (0,0,0) domain hc xform translation = [ 0.15334 -0.208601 -0.332707 ] domain hc backbone color = [ 1 0 0 ] width = 1 show domain create hj = C domain hj xform translation = [ 3.15334 -0.208601 -0.332707 ] domain hj backbone color = [ 0 1 0 ] width = 1 show # create cylinders #----------------- solid create name = cyl1 type = cylinder \ radius = 0.22 \ domain = hc \ region = C[762-780] \ atoms = { CA } \ color = [ 1 0 0 ] \ display = line \ show = true solid create name = cyl2 type = cylinder \ radius = 0.22 \ domain = hc \ region = C[780-796] \ atoms = { CA } \ allign = cyl1 \ color = [ 0 1 0 ] \ display = line \ show = true solid create name = cyl3 type = cylinder \ radius = 0.22 \ domain = hc \ region = C[796-814] \ atoms = { CA } \ allign = cyl2 \ color = [ 1 1 0 ] \ display = line \ show = true solid create name = cyl4 type = cylinder \ radius = 0.22 \ domain = hc \ region = C[814-832] \ atoms = { CA } \ allign = cyl3 \ color = [ 0 1 1 ] \ display = line \ show = true #--- 2nd helix ---- solid create name = cyl5 type = cylinder \ radius = 0.22 \ domain = hj \ region = C[762-780] \ atoms = { CA } \ color = [ 1 0 0 ] \ display = line \ show = true solid create name = cyl6 type = cylinder \ radius = 0.22 \ domain = hj \ region = C[780-796] \ atoms = { CA } \ allign = cyl5 \ color = [ 0 1 0 ] \ display = line \ show = true solid create name = cyl7 type = cylinder \ radius = 0.22 \ domain = hj \ region = C[796-814] \ atoms = { CA } \ allign = cyl6 \ color = [ 1 1 0 ] \ display = line \ show = true solid create name = cyl8 type = cylinder \ radius = 0.22 \ domain = hj \ region = C[814-832] \ atoms = { CA } \ allign = cyl7 \ color = [ 0 1 1 ] \ display = line \ show = true # create bodies #-------------- body create name = ground type = ground body create name = cyl1_body type = rigid solid = cyl1 body create name = cyl2_body type = rigid solid = cyl2 body create name = cyl3_body type = rigid solid = cyl3 body create name = cyl4_body type = rigid solid = cyl4 #--- 2nd helix ---- body create name = cyl5_body type = rigid solid = cyl5 body create name = cyl6_body type = rigid solid = cyl6 body create name = cyl7_body type = rigid solid = cyl7 body create name = cyl8_body type = rigid solid = cyl8 # create joints #-------------- joint create name = jnt1 type = ball cylinder = cyl1 distance = 0.0 joint jnt1 color = [ 1 1 1 ] msize = 0.1 shading = color show = true joint jnt1 bodies = { ground cyl1_body } joint create name = jnt2 type = ball cylinder = cyl1 distance = 1.0 joint jnt2 color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint jnt2 bodies = { cyl1_body cyl2_body } joint create name = jnt3 type = ball cylinder = cyl2 distance = 1.0 joint jnt3 color = [ 0 1 0 ] msize = 0.1 shading = color show = true joint jnt3 bodies = { cyl2_body cyl3_body } joint create name = jnt4 type = ball cylinder = cyl3 distance = 1.0 joint jnt4 color = [ 1 1 0 ] msize = 0.1 shading = color show = true joint jnt4 bodies = { cyl3_body cyl4_body } #--- 2nd helix ---- joint create name = jnt5 type = ball cylinder = cyl5 distance = 0.0 joint jnt5 color = [ 1 1 1 ] msize = 0.1 shading = color show = true joint jnt5 bodies = { ground cyl5_body } joint create name = jnt6 type = ball cylinder = cyl6 distance = 0.0 joint jnt6 color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint jnt6 bodies = { cyl5_body cyl6_body } joint create name = jnt7 type = ball cylinder = cyl7 distance = 0.0 joint jnt7 color = [ 0 1 0 ] msize = 0.1 shading = color show = true joint jnt7 bodies = { cyl6_body cyl7_body } joint create name = jnt8 type = ball cylinder = cyl8 distance = 0.0 joint jnt8 color = [ 1 1 0 ] msize = 0.1 shading = color show = true joint jnt8 bodies = { cyl7_body cyl8_body } # create a rigid simulation #-------------------------- simulation create name = rsim type = rigid # set solver #----------- simulation rsim solver = ode simulation rsim solver finite_rotation = on # add bodies #----------- simulation rsim add body = ground simulation rsim add body = cyl1_body simulation rsim add body = cyl2_body simulation rsim add body = cyl3_body simulation rsim add body = cyl4_body simulation rsim add body = cyl5_body simulation rsim add body = cyl6_body simulation rsim add body = cyl7_body simulation rsim add body = cyl8_body # add joints #----------- simulation rsim add joint = jnt1 simulation rsim add joint = jnt2 simulation rsim add joint = jnt3 simulation rsim add joint = jnt4 simulation rsim add joint = jnt5 simulation rsim add joint = jnt6 simulation rsim add joint = jnt7 simulation rsim add joint = jnt8 # add forces #----------- force create name = force1 \ type = explicit \ point = [ 0 0 0 ] \ direction = [ 1 0 0 ] \ scale = 1.0 \ show = true simulation rsim add force = force1 \ body = cyl4_body \ time = { 0 1000 } force create name = force2 \ type = explicit \ point = [ 0 0 0 ] \ direction = [ -1 0 0 ] \ scale = 1.0 #simulation rsim add force = force2 \ body = cyl8_body \ time = { 0 1000 } # add interaction potentials #--------------------------- solid cyl4 define region = cyl4_rgn body cyl4_body add potential = cyl4_contact \ type = contact \ region = cyl4_rgn \ geometry = cylinder \ strength = 40.0 \ show = true solid cyl8 define region = cyl8_rgn body cyl8_body add potential = cyl8_contact \ type = contact \ region = cyl8_rgn \ geometry = cylinder \ strength = 20.0 \ show = true simulation rsim add interaction = contact1 \ body1 = cyl4_body potential1 = cyl4_contact \ body2 = cyl8_body potential2 = cyl8_contact \ time = { 0.0 1000.0 } # initialize simulation #---------------------- simulation rsim initialize simulation rsim time step = 0.002 # step simulation #---------------- #simulation rsim step = 305 simulation rsim step = 520