Added source code and documentation for USER-CGDNA
This commit is contained in:
Oliver Henrich
28
examples/USER/cgdna/README
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28
examples/USER/cgdna/README
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This directory contains example data and input files
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and utility scripts for the oxDNA coarse-grained model
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for DNA.
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/examples/duplex1:
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Input, data and log files for a DNA duplex (double-stranded DNA)
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consisiting of 5 base pairs. The duplex contains two strands with
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complementary base pairs. The topology is
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A - A - A - A - A
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| | | | |
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T - T - T - T - T
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/examples/duplex2:
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Input, data and log files for a nicked DNA duplex (double-stranded DNA)
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consisiting of 8 base pairs. The duplex contains strands with
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complementary base pairs, but the backbone on one side is not continuous:
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two individual strands on one side form a duplex with a longer single
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strand on the other side. The topology is
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A - A - A - A - A - A - A - A
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| | | | | | | |
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T - T - T T - T - T - T - T
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/util:
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This directory contains a simple python setup tool which creates
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single straight or helical DNA strands, DNA duplexes or arrays of DNA
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duplexes.
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74
examples/USER/cgdna/examples/duplex1/data.duplex1
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74
examples/USER/cgdna/examples/duplex1/data.duplex1
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# LAMMPS data file
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10 atoms
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10 ellipsoids
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8 bonds
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4 atom types
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1 bond types
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# System size
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-20.000000 20.000000 xlo xhi
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-20.000000 20.000000 ylo yhi
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-20.000000 20.000000 zlo zhi
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# Atom masses for each atom type
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Masses
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1 3.1575
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2 3.1575
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3 3.1575
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4 3.1575
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# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
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Atoms
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1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
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2 1 1.3274493266864451e-01 -4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
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3 1 4.8460810659772807e-01 -7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
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4 1 9.3267359196674593e-01 -7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
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5 1 1.3204192238113461e+00 -5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
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6 4 1.9958077618865377e-01 5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
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7 4 5.8732640803325409e-01 7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
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8 4 1.0353918934022719e+00 7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
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9 4 1.3872550673313555e+00 4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
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10 4 1.5200000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
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# Atom-ID, translational, rotational velocity
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Velocities
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1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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# Atom-ID, shape, quaternion
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Ellipsoids
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1 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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2 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 9.5533648912560598e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.9552020666133955e-01
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3 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 8.2533561490967822e-01 0.0000000000000000e+00 0.0000000000000000e+00 5.6464247339503526e-01
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4 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 6.2160996827066439e-01 0.0000000000000000e+00 0.0000000000000000e+00 7.8332690962748319e-01
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5 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 3.6235775447667351e-01 0.0000000000000000e+00 0.0000000000000000e+00 9.3203908596722607e-01
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6 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 9.3203908596722607e-01 -3.6235775447667351e-01 0.0000000000000000e+00
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7 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 7.8332690962748319e-01 -6.2160996827066439e-01 0.0000000000000000e+00
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8 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 5.6464247339503526e-01 -8.2533561490967822e-01 0.0000000000000000e+00
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9 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 2.9552020666133955e-01 -9.5533648912560598e-01 0.0000000000000000e+00
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10 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00
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# Bond topology
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Bonds
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1 1 1 2
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2 1 2 3
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3 1 3 4
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4 1 4 5
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5 1 6 7
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6 1 7 8
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7 1 8 9
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8 1 9 10
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77
examples/USER/cgdna/examples/duplex1/input.duplex1
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77
examples/USER/cgdna/examples/duplex1/input.duplex1
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variable number equal 1
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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.duplex1
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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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1163
examples/USER/cgdna/examples/duplex1/log.duplex1_1p
Normal file
1163
examples/USER/cgdna/examples/duplex1/log.duplex1_1p
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File diff suppressed because it is too large
Load Diff
1163
examples/USER/cgdna/examples/duplex1/log.duplex1_8p
Normal file
1163
examples/USER/cgdna/examples/duplex1/log.duplex1_8p
Normal file
File diff suppressed because it is too large
Load Diff
97
examples/USER/cgdna/examples/duplex2/data.duplex2
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97
examples/USER/cgdna/examples/duplex2/data.duplex2
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@ -0,0 +1,97 @@
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# LAMMPS data file
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16 atoms
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16 ellipsoids
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13 bonds
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4 atom types
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1 bond types
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# System size
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-20.0 20.0 xlo xhi
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-20.0 20.0 ylo yhi
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-20.0 20.0 zlo zhi
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# Atom masses for each atom type
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Masses
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1 3.1575
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2 3.1575
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3 3.1575
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4 3.1575
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# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
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Atoms
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1 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1 1 1
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2 1 1.327449326686445e-01 -4.291282797802268e-01 3.750616346940281e-01 1 1 1
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3 1 4.846081065977281e-01 -7.083497053350921e-01 7.501232693880562e-01 1 1 1
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4 1 9.326735919667459e-01 -7.401241994674285e-01 1.125184904082084e+00 1 1 1
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5 1 1.320419223811347e+00 -5.133520172188747e-01 1.500246538776112e+00 1 1 1
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6 1 1.512394297416339e+00 -1.072512061254991e-01 1.875308173470140e+00 1 1 1
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7 1 1.441536396413952e+00 3.363155369040876e-01 2.250369808164169e+00 1 1 1
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8 1 1.132598224218932e+00 6.623975870343269e-01 2.625431442858197e+00 1 1 1
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9 4 5.873264080332541e-01 7.401241994674285e-01 1.125184904082084e+00 1 1 1
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10 4 1.035391893402272e+00 7.083497053350921e-01 7.501232693880562e-01 1 1 1
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11 4 1.387255067331356e+00 4.291282797802267e-01 3.750616346940281e-01 1 1 1
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||||
12 4 1.520000000000000e+00 1.260981291332700e-33 0.000000000000000e+00 1 1 1
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||||
13 4 3.874017757810680e-01 -6.623975870343268e-01 2.625431442858197e+00 1 1 1
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14 4 7.846360358604798e-02 -3.363155369040874e-01 2.250369808164169e+00 1 1 1
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15 4 7.605702583661333e-03 1.072512061254995e-01 1.875308173470140e+00 1 1 1
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||||
16 4 1.995807761886533e-01 5.133520172188748e-01 1.500246538776112e+00 1 1 1
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# Atom-ID, translational, rotational velocity
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Velocities
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1 0.0 0.0 0.0 0.0 0.0 0.0
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2 0.0 0.0 0.0 0.0 0.0 0.0
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||||
3 0.0 0.0 0.0 0.0 0.0 0.0
|
||||
4 0.0 0.0 0.0 0.0 0.0 0.0
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||||
5 0.0 0.0 0.0 0.0 0.0 0.0
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6 0.0 0.0 0.0 0.0 0.0 0.0
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||||
7 0.0 0.0 0.0 0.0 0.0 0.0
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8 0.0 0.0 0.0 0.0 0.0 0.0
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||||
9 0.0 0.0 0.0 0.0 0.0 0.0
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||||
10 0.0 0.0 0.0 0.0 0.0 0.0
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||||
11 0.0 0.0 0.0 0.0 0.0 0.0
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||||
12 0.0 0.0 0.0 0.0 0.0 0.0
|
||||
13 0.0 0.0 0.0 0.0 0.0 0.0
|
||||
14 0.0 0.0 0.0 0.0 0.0 0.0
|
||||
15 0.0 0.0 0.0 0.0 0.0 0.0
|
||||
16 0.0 0.0 0.0 0.0 0.0 0.0
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||||
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||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.1739845031423408 1.1739845031423408 1.1739845031423408 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.1739845031423408 1.1739845031423408 1.1739845031423408 9.553364891256060e-01 0.000000000000000e+00 0.000000000000000e+00 2.955202066613395e-01
|
||||
3 1.1739845031423408 1.1739845031423408 1.1739845031423408 8.253356149096783e-01 0.000000000000000e+00 0.000000000000000e+00 5.646424733950354e-01
|
||||
4 1.1739845031423408 1.1739845031423408 1.1739845031423408 6.216099682706646e-01 0.000000000000000e+00 0.000000000000000e+00 7.833269096274833e-01
|
||||
5 1.1739845031423408 1.1739845031423408 1.1739845031423408 3.623577544766736e-01 0.000000000000000e+00 0.000000000000000e+00 9.320390859672263e-01
|
||||
6 1.1739845031423408 1.1739845031423408 1.1739845031423408 7.073720166770291e-02 0.000000000000000e+00 0.000000000000000e+00 9.974949866040544e-01
|
||||
7 1.1739845031423408 1.1739845031423408 1.1739845031423408 -2.272020946930869e-01 -0.000000000000000e+00 0.000000000000000e+00 9.738476308781953e-01
|
||||
8 1.1739845031423408 1.1739845031423408 1.1739845031423408 -5.048461045998575e-01 -0.000000000000000e+00 0.000000000000000e+00 8.632093666488738e-01
|
||||
9 1.1739845031423408 1.1739845031423408 1.1739845031423408 4.796493962806427e-17 7.833269096274833e-01 -6.216099682706646e-01 3.806263289803786e-17
|
||||
10 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.707093416549944e-17 5.646424733950354e-01 -8.253356149096784e-01 2.218801320830406e-17
|
||||
11 1.1739845031423408 1.1739845031423408 1.1739845031423408 6.107895212550935e-17 2.955202066613394e-01 -9.553364891256061e-01 4.331404380149668e-18
|
||||
12 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.963096920061075e-17 0.000000000000000e+00 -1.000000000000000e+00 -1.391211590127312e-17
|
||||
13 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.285632939302787e-17 8.632093666488739e-01 5.048461045998572e-01 -3.091290830301125e-17
|
||||
14 1.1739845031423408 1.1739845031423408 1.1739845031423408 4.136019110019290e-17 9.738476308781953e-01 2.272020946930868e-01 -4.515234267244800e-17
|
||||
15 1.1739845031423408 1.1739845031423408 1.1739845031423408 2.616947011741696e-17 9.974949866040544e-01 -7.073720166770313e-02 -5.535845274597425e-17
|
||||
16 1.1739845031423408 1.1739845031423408 1.1739845031423408 8.641108308308281e-18 9.320390859672264e-01 -3.623577544766736e-01 -6.061955710708163e-17
|
||||
|
||||
# Bond-ID, type, atom pairs
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 13 14
|
||||
9 1 14 15
|
||||
10 1 15 16
|
||||
11 1 9 10
|
||||
12 1 10 11
|
||||
13 1 11 12
|
||||
77
examples/USER/cgdna/examples/duplex2/input.duplex2
Normal file
77
examples/USER/cgdna/examples/duplex2/input.duplex2
Normal file
@ -0,0 +1,77 @@
|
||||
variable number equal 2
|
||||
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}.*
|
||||
1163
examples/USER/cgdna/examples/duplex2/log.duplex2_1p
Normal file
1163
examples/USER/cgdna/examples/duplex2/log.duplex2_1p
Normal file
File diff suppressed because it is too large
Load Diff
1163
examples/USER/cgdna/examples/duplex2/log.duplex2_8p
Normal file
1163
examples/USER/cgdna/examples/duplex2/log.duplex2_8p
Normal file
File diff suppressed because it is too large
Load Diff
388
examples/USER/cgdna/util/generate_input.py
Normal file
388
examples/USER/cgdna/util/generate_input.py
Normal file
@ -0,0 +1,388 @@
|
||||
# Setup tool for oxDNA input in LAMMPS format.
|
||||
|
||||
import math,numpy as np,sys,os
|
||||
|
||||
# system size
|
||||
lxmin = -115.0
|
||||
lxmax = +115.0
|
||||
lymin = -115.0
|
||||
lymax = +115.0
|
||||
lzmin = -115.0
|
||||
lzmax = +115.0
|
||||
|
||||
# rise in z-direction
|
||||
r0 = 0.7
|
||||
|
||||
# definition of single untwisted strand
|
||||
def single():
|
||||
|
||||
strand = inp[1].split(':')
|
||||
|
||||
com_start=strand[0].split(',')
|
||||
|
||||
posx=float(com_start[0])
|
||||
posy=float(com_start[1])
|
||||
posz=float(com_start[2])
|
||||
risex=0
|
||||
risey=0
|
||||
risez=r0
|
||||
|
||||
strandstart=len(nucleotide)+1
|
||||
|
||||
for letter in strand[2]:
|
||||
temp=[]
|
||||
|
||||
temp.append(nt2num[letter])
|
||||
temp.append([posx,posy,posz])
|
||||
vel=[0,0,0,0,0,0]
|
||||
temp.append(vel)
|
||||
temp.append(shape)
|
||||
|
||||
quat=[1,0,0,0]
|
||||
temp.append(quat)
|
||||
|
||||
posx=posx+risex
|
||||
posy=posy+risey
|
||||
posz=posz+risez
|
||||
|
||||
if (len(nucleotide)+1 > strandstart):
|
||||
topology.append([1,len(nucleotide),len(nucleotide)+1])
|
||||
|
||||
nucleotide.append(temp)
|
||||
|
||||
return
|
||||
|
||||
# definition of single twisted strand
|
||||
def single_helix():
|
||||
|
||||
strand = inp[1].split(':')
|
||||
|
||||
com_start=strand[0].split(',')
|
||||
twist=float(strand[1])
|
||||
|
||||
posx = float(com_start[0])
|
||||
posy = float(com_start[1])
|
||||
posz = float(com_start[2])
|
||||
risex=0
|
||||
risey=0
|
||||
risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2)
|
||||
|
||||
dcomh=0.76
|
||||
axisx=dcomh + posx
|
||||
axisy=posy
|
||||
|
||||
strandstart=len(nucleotide)+1
|
||||
quat=[1,0,0,0]
|
||||
|
||||
qrot0=math.cos(0.5*twist)
|
||||
qrot1=0
|
||||
qrot2=0
|
||||
qrot3=math.sin(0.5*twist)
|
||||
|
||||
for letter in strand[2]:
|
||||
temp=[]
|
||||
|
||||
temp.append(nt2num[letter])
|
||||
temp.append([posx,posy,posz])
|
||||
vel=[0,0,0,0,0,0]
|
||||
temp.append(vel)
|
||||
temp.append(shape)
|
||||
|
||||
temp.append(quat)
|
||||
|
||||
quat0 = quat[0]*qrot0 - quat[1]*qrot1 - quat[2]*qrot2 - quat[3]*qrot3
|
||||
quat1 = quat[0]*qrot1 + quat[1]*qrot0 + quat[2]*qrot3 - quat[3]*qrot2
|
||||
quat2 = quat[0]*qrot2 + quat[2]*qrot0 + quat[3]*qrot1 - quat[1]*qrot3
|
||||
quat3 = quat[0]*qrot3 + quat[3]*qrot0 + quat[1]*qrot2 + quat[2]*qrot1
|
||||
|
||||
quat = [quat0,quat1,quat2,quat3]
|
||||
|
||||
posx=axisx - dcomh*(quat[0]**2+quat[1]**2-quat[2]**2-quat[3]**2)
|
||||
posy=axisy - dcomh*(2*(quat[1]*quat[2]+quat[0]*quat[3]))
|
||||
posz=posz+risez
|
||||
|
||||
if (len(nucleotide)+1 > strandstart):
|
||||
topology.append([1,len(nucleotide),len(nucleotide)+1])
|
||||
|
||||
nucleotide.append(temp)
|
||||
|
||||
return
|
||||
|
||||
# definition of twisted duplex
|
||||
def duplex():
|
||||
|
||||
strand = inp[1].split(':')
|
||||
|
||||
com_start=strand[0].split(',')
|
||||
twist=float(strand[1])
|
||||
|
||||
compstrand=[]
|
||||
comptopo=[]
|
||||
|
||||
posx1 = float(com_start[0])
|
||||
posy1 = float(com_start[1])
|
||||
posz1 = float(com_start[2])
|
||||
|
||||
risex=0
|
||||
risey=0
|
||||
risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2)
|
||||
|
||||
dcomh=0.76
|
||||
axisx=dcomh + posx1
|
||||
axisy=posy1
|
||||
|
||||
posx2 = axisx + dcomh
|
||||
posy2 = posy1
|
||||
posz2 = posz1
|
||||
|
||||
strandstart=len(nucleotide)+1
|
||||
|
||||
quat1=[1,0,0,0]
|
||||
quat2=[0,0,-1,0]
|
||||
|
||||
qrot0=math.cos(0.5*twist)
|
||||
qrot1=0
|
||||
qrot2=0
|
||||
qrot3=math.sin(0.5*twist)
|
||||
|
||||
for letter in strand[2]:
|
||||
temp1=[]
|
||||
temp2=[]
|
||||
|
||||
temp1.append(nt2num[letter])
|
||||
temp2.append(compnt2num[letter])
|
||||
|
||||
temp1.append([posx1,posy1,posz1])
|
||||
temp2.append([posx2,posy2,posz2])
|
||||
|
||||
vel=[0,0,0,0,0,0]
|
||||
temp1.append(vel)
|
||||
temp2.append(vel)
|
||||
|
||||
temp1.append(shape)
|
||||
temp2.append(shape)
|
||||
|
||||
temp1.append(quat1)
|
||||
temp2.append(quat2)
|
||||
|
||||
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
|
||||
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
|
||||
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
|
||||
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
|
||||
|
||||
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
|
||||
|
||||
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz1=posz1+risez
|
||||
|
||||
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
|
||||
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
|
||||
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
|
||||
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
|
||||
|
||||
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
|
||||
|
||||
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz2=posz1
|
||||
|
||||
if (len(nucleotide)+1 > strandstart):
|
||||
topology.append([1,len(nucleotide),len(nucleotide)+1])
|
||||
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
|
||||
|
||||
nucleotide.append(temp1)
|
||||
compstrand.append(temp2)
|
||||
|
||||
for ib in range(len(compstrand)):
|
||||
nucleotide.append(compstrand[len(compstrand)-1-ib])
|
||||
|
||||
for ib in range(len(comptopo)):
|
||||
topology.append(comptopo[ib])
|
||||
|
||||
return
|
||||
|
||||
# definition of array of duplexes
|
||||
def duplex_array():
|
||||
|
||||
strand = inp[1].split(':')
|
||||
number=strand[0].split(',')
|
||||
posz1_0 = float(strand[1])
|
||||
twist=float(strand[2])
|
||||
|
||||
nx = int(number[0])
|
||||
ny = int(number[1])
|
||||
|
||||
dx = (lxmax-lxmin)/nx
|
||||
dy = (lymax-lymin)/ny
|
||||
|
||||
risex=0
|
||||
risey=0
|
||||
risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2)
|
||||
dcomh=0.76
|
||||
|
||||
for ix in range(nx):
|
||||
|
||||
axisx=lxmin + dx/2 + ix * dx
|
||||
|
||||
for iy in range(ny):
|
||||
|
||||
axisy=lymin + dy/2 + iy * dy
|
||||
|
||||
compstrand=[]
|
||||
comptopo=[]
|
||||
|
||||
posx1 = axisx - dcomh
|
||||
posy1 = axisy
|
||||
posz1 = posz1_0
|
||||
|
||||
posx2 = axisx + dcomh
|
||||
posy2 = posy1
|
||||
posz2 = posz1
|
||||
|
||||
strandstart=len(nucleotide)+1
|
||||
quat1=[1,0,0,0]
|
||||
quat2=[0,0,-1,0]
|
||||
|
||||
qrot0=math.cos(0.5*twist)
|
||||
qrot1=0
|
||||
qrot2=0
|
||||
qrot3=math.sin(0.5*twist)
|
||||
|
||||
for letter in strand[3]:
|
||||
temp1=[]
|
||||
temp2=[]
|
||||
|
||||
temp1.append(nt2num[letter])
|
||||
temp2.append(compnt2num[letter])
|
||||
|
||||
temp1.append([posx1,posy1,posz1])
|
||||
temp2.append([posx2,posy2,posz2])
|
||||
|
||||
vel=[0,0,0,0,0,0]
|
||||
temp1.append(vel)
|
||||
temp2.append(vel)
|
||||
|
||||
temp1.append(shape)
|
||||
temp2.append(shape)
|
||||
|
||||
temp1.append(quat1)
|
||||
temp2.append(quat2)
|
||||
|
||||
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
|
||||
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
|
||||
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
|
||||
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
|
||||
|
||||
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
|
||||
|
||||
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz1=posz1+risez
|
||||
|
||||
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
|
||||
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
|
||||
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
|
||||
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
|
||||
|
||||
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
|
||||
|
||||
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz2=posz1
|
||||
|
||||
if (len(nucleotide)+1 > strandstart):
|
||||
topology.append([1,len(nucleotide),len(nucleotide)+1])
|
||||
comptopo.append([1,len(nucleotide)+len(strand[3]),len(nucleotide)+len(strand[3])+1])
|
||||
|
||||
nucleotide.append(temp1)
|
||||
compstrand.append(temp2)
|
||||
|
||||
for ib in range(len(compstrand)):
|
||||
nucleotide.append(compstrand[len(compstrand)-1-ib])
|
||||
|
||||
for ib in range(len(comptopo)):
|
||||
topology.append(comptopo[ib])
|
||||
|
||||
return
|
||||
|
||||
# main part
|
||||
nt2num = {'A':1, 'C':2, 'G':3, 'T':4}
|
||||
compnt2num = {'T':1, 'G':2, 'C':3, 'A':4}
|
||||
shape = [1.1739845031423408,1.1739845031423408,1.1739845031423408]
|
||||
|
||||
nucleotide=[]
|
||||
topology=[]
|
||||
|
||||
seqfile = open(sys.argv[1],'r')
|
||||
|
||||
# process sequence file line by line
|
||||
for line in seqfile:
|
||||
|
||||
inp = line.split()
|
||||
if inp[0] == 'single':
|
||||
single()
|
||||
if inp[0] == 'single_helix':
|
||||
single_helix()
|
||||
if inp[0] == 'duplex':
|
||||
duplex()
|
||||
if inp[0] == 'duplex_array':
|
||||
duplex_array()
|
||||
|
||||
# output atom data in LAMMPS format
|
||||
out = open(sys.argv[2],'w')
|
||||
|
||||
out.write('# LAMMPS data file\n')
|
||||
out.write('%d atoms\n' % len(nucleotide))
|
||||
out.write('%d ellipsoids\n' % len(nucleotide))
|
||||
out.write('%d bonds\n' % len(topology))
|
||||
out.write('\n')
|
||||
out.write('4 atom types\n')
|
||||
out.write('1 bond types\n')
|
||||
out.write('\n')
|
||||
out.write('# System size\n')
|
||||
out.write('%f %f xlo xhi\n' % (lxmin,lxmax))
|
||||
out.write('%f %f ylo yhi\n' % (lymin,lymax))
|
||||
out.write('%f %f zlo zhi\n' % (lzmin,lzmax))
|
||||
out.write('\n')
|
||||
out.write('Masses\n')
|
||||
out.write('\n')
|
||||
out.write('1 3.1575\n')
|
||||
out.write('2 3.1575\n')
|
||||
out.write('3 3.1575\n')
|
||||
out.write('4 3.1575\n')
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
|
||||
out.write('Atoms\n')
|
||||
out.write('\n')
|
||||
for ib in range(len(nucleotide)):
|
||||
out.write("%d %d %22.16le %22.16le %22.16le 1 1 1\n" % (ib+1,nucleotide[ib][0],nucleotide[ib][1][0],nucleotide[ib][1][1],nucleotide[ib][1][2]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, translational, rotational velocity\n')
|
||||
out.write('Velocities\n')
|
||||
out.write('\n')
|
||||
for ib in range(len(nucleotide)):
|
||||
out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][2][0],nucleotide[ib][2][1],nucleotide[ib][2][2],nucleotide[ib][2][3],nucleotide[ib][2][4],nucleotide[ib][2][5]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, shape, quaternion\n')
|
||||
out.write('Ellipsoids\n')
|
||||
out.write('\n')
|
||||
for ib in range(len(nucleotide)):
|
||||
out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][3][0],nucleotide[ib][3][1],nucleotide[ib][3][2],nucleotide[ib][4][0],nucleotide[ib][4][1],nucleotide[ib][4][2],nucleotide[ib][4][3]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Bond topology\n')
|
||||
out.write('Bonds\n')
|
||||
out.write('\n')
|
||||
for ib in range(len(topology)):
|
||||
out.write("%d %d %d %d\n" % (ib+1,topology[ib][0],topology[ib][1],topology[ib][2]))
|
||||
|
||||
out.close()
|
||||
|
||||
seqfile.close()
|
||||
sys.exit(0)
|
||||
|
||||
|
||||
77
examples/USER/cgdna/util/input.ref
Normal file
77
examples/USER/cgdna/util/input.ref
Normal file
@ -0,0 +1,77 @@
|
||||
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}.*
|
||||
4
examples/USER/cgdna/util/sequence.txt
Normal file
4
examples/USER/cgdna/util/sequence.txt
Normal file
@ -0,0 +1,4 @@
|
||||
single 0,0,0:0.6:AAAAA
|
||||
single_helix 0,0,0:0.6:AAAAA
|
||||
duplex 0,0,0:0.6:AAAAA
|
||||
duplex_array 10,10:-112.0:0.6:AAAAA
|
||||
Reference in New Issue
Block a user