#######################Init Section######################
units           real
boundary p p p
atom_style      full
bond_style      harmonic
angle_style     hybrid harmonic cosine 
read_data SH3_PRM_100uM.data extra/special/per/atom 10
pair_style lj/cut 10

pair_coeff 1 1 0.25 4.2 4.2
pair_coeff 2 2 0.25 20 20
pair_coeff 3 3 0.25 4.2 4.2
pair_coeff 4 4 0.25 20 20
pair_coeff 1 2 0.25 12.1 12.1
pair_coeff 1 4 0.25 12.1 12.1
pair_coeff 2 3 0.25 12.1 12.1
pair_coeff 3 4 0.25 12.1 12.1

pair_coeff 2 4 0.15 20 50
pair_coeff 1 3 0.6 4.2 10.5

bond_coeff *          1 21
bond_coeff 1          2 4.3
bond_coeff 2          2 12.1
bond_coeff 4          2 12.1
bond_coeff 3          2 4.3
bond_coeff 5          1 23

angle_coeff  * cosine      2
#fix rigbonds all rattle 0.0001 20 0 b 1 2 3 4
special_bonds lj 0 0.2 0.5 angle no
compute 1 all temp

thermo          10000
group sh3 type 2 4

minimize 1.0e-5 1.0e-7 100000 100000

############################Langevin Dynamics###############################
#neigh_modify every 1 delay 2 check yes
fix fxlan all langevin 310.0 310.0 1500 48279
fix fxnve all nve 
fix bondc sh3 bond/create 20 2 4 23.7 5 prob 1 49829 iparam 1 2 jparam 1 4
fix bondbr sh3 bond/break 20 5 24.2 prob 1 49629
thermo_style    custom step ebond etotal temp f_bondc[1] f_bondc[2]
timestep 25

restart 30000 sim.1.restart sim.2.restart
dump dyn all dcd 30000 sh3_prm.dcd
dump_modify dyn unwrap yes
run   5000000
write_data sh3_prm_equi.data
undump dyn