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