variable number equal 2
variable ofreq equal 10000
variable efreq equal 10000
variable T equal 0.1
variable seed equal 123456789

units lj

dimension 3

newton on

boundary p p p

atom_style hybrid bond ellipsoid oxdna
atom_modify sort 0 1.0

# Pair interactions require lists of neighbours to be calculated
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes

read_data init.conf.lammps

set atom * mass 3.1575

group all type 1 4

# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0000 0.2500 0.7564
special_bonds lj 0 1 1

# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk     seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh      ${T} 0.5 0.815

# NVE ensemble
fix 1 all nve/asphere
fix 2 all langevin ${T} ${T} 2.5 ${seed} angmom 10

timestep 0.003

#comm_style tiled
fix 3 all balance 1000 1.03 shift xyz 10 1.03
comm_modify cutoff 3.8

compute quat all property/atom quatw quati quatj quatk

compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot

dump mythos-out all custom ${ofreq} trajectory.dat id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump_modify mythos-out sort id
dump_modify mythos-out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"


thermo_style custom step pe
thermo ${ofreq}

run 250000

write_data last_config.${number}.* nocoeff