clear
variable SEED_1 equal 54654651 
variable    a loop 4
log        log.$a

units real 
atom_style full
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 10 delay 0 check yes

lattice sc 1.0
region myregion1 block 0 30 0 30 0 30 units box 

read_data dataconfiguration28.LAMMPS

# his is histone
# poly and poly2 are DNA
# poly1 is 14  contact.points 

group his type 1 
group poly type 2
group poly1 type 3
group poly2 type 2 3

bond_style   fene
special_bonds fene
bond_coeff   1  30.0  1.5  1.0   1.0 

pair_style hybrid/overlay lj/cut 1.12 morse 3.0 coul/debye 1.4 3.0
pair_coeff 1 1 lj/cut 1.0 1.0 1.12
pair_coeff 1 2 morse 0.0 0.30 3.
pair_coeff 1 3 lj/cut 1.0 1.0 1.12
pair_coeff 2 2 coul/debye 3.5 
pair_coeff 2 3 morse 0.1 3.0 3.
pair_coeff 3 3 lj/cut 1.0 1.0 1.12  

velocity all create 1 176217 dist gaussian

# DELETE OVERLAPPING ATOMS:
delete_atoms overlap 0.5 poly1 his
delete_atoms overlap 0.5 poly his

fix FREEZE1 his  setforce 0.0 0.0 0.0
fix FREEZE2 poly  setforce 0.0 0.0 0.0

timestep 0.005
minimize 0.0 1.0e-4 1000 100000

fix NVE poly nve
fix LANGEVIN poly langevin 1.0 1.1  1 ${SEED_1}

compute msd_col poly msd
compute 1 all pe
variable t equal step
variable MYTEMP equal temp
variable MYEPAIR equal epair

dump DUMPXYZ all xyz 50 outff30.xyz
dump positions all atom 100 outf2.lammpstrj
dump myDUMP  poly2 xyz 50 outff31.xyz

fix MYTHERMOFILE all print 1000 "$t ${MYTEMP} ${MYEPAIR} " file thermo_output.dat screen no

timestep 0.005

thermo_style custom step temp pe ke etotal c_msd_col[1] c_msd_col[2] c_msd_col[3]  c_msd_col[4] 
thermo 1000

run 50000
undump DUMPXYZ

next  a
jump  chromatinfinal1.in
echo both