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lammps/examples/USER/cgdna/util/input.ref
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variable number equal 8
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
processors 1 1 1
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
set atom * mass 3.1575
group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna_fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 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 * * oxdna_hbond 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 oxdna_hbond 1.077 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 oxdna_hbond 1.077 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 * * oxdna_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 * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
fix 1 all nve/dot
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
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
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
dump_modify out sort id
dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
#write_restart config.${number}.*
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