73 lines
2.7 KiB
Plaintext
73 lines
2.7 KiB
Plaintext
variable number equal 5
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 0.1
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variable rhos equal 0.2
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units lj
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dimension 3
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newton on
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boundary p p p
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atom_style hybrid bond ellipsoid oxdna
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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 2.0 bin
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neigh_modify every 1 delay 0 check yes
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read_data data.dsring
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set atom * mass 3.1575
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group all type 1 4
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# oxDNA2 bond interactions - FENE backbone
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bond_style oxdna2/fene
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bond_coeff * 2.0 0.25 0.7564
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special_bonds lj 0 1 1
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# oxDNA2 pair interactions
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pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
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pair_coeff * * oxdna2/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 * * oxdna2/stk seqdep ${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
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pair_coeff * * oxdna2/hbond seqdep 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 oxdna2/hbond seqdep 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
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pair_coeff 2 3 oxdna2/hbond seqdep 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
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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
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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
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pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
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# NVE ensemble
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fix 1 all nve/asphere
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#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
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timestep 1e-5
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#comm_style tiled
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fix 3 all balance 1000 1.03 shift xyz 10 1.03
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comm_modify cutoff 3.8
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compute quat all property/atom quatw quati quatj quatk
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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}.lammpstrj 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
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dump_modify out sort id
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dump_modify 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"
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run 100000
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write_data last_config.${number}.* nocoeff
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#write_restart last_config.${number}.*
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