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run_settings.txt
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run_settings.txt
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compute q dna property/atom quatw quati quatj quatk
compute shape dna property/atom shapex shapey shapez
dump 1 all custom 1000 dna.dump &
id x y z c_q[1] c_q[2] c_q[3] c_q[4] &
c_shape[1] c_shape[2] c_shape[3] mol q type
dump_modify 1 sort id
comm_style tiled
thermo_style custom step temp pe epair ebond ke etotal spcpu
thermo 1000
# minimize first
fix 1 notdna nve
fix 2 notdna viscous 1000000.0
#fix spring1
timestep 0.0001
run 1000
timestep 0.001
run 1000
timestep 0.01
run 1000
unfix 2
fix 2 notdna viscous 10000.0
timestep 0.1
run 1000
timestep 5.0
run 1000
timestep 10.0
run 1000
unfix 1
unfix 2
fix 2 notdna langevin 300.0 300.0 1000.0 123 gjf vhalf
fix 1 notdna nve
fix 3 dna_all rigid/nve/small molecule
fix 4 dna langevin 300.0 300.0 1000.0 123 angmom 3.0
fix bl all balance 1000 1.0 rcb
#fix C all recenter INIT INIT INIT
run 10000
timestep 10.0
fix 2 notdna langevin 300.0 300.0 10000.0 123 gjf vhalf
fix 4 dna langevin 300.0 300.0 10000.0 123 angmom 3.0
fix pull1 end1 drag 0 0 -10000 1.0 0.0
fix pull2 end2 drag 0 0 10000 1.0 0.0
timestep 20.0
run 10000
unfix 1
unfix 2
unfix 3
unfix 4
unfix bl
unfix pull1
unfix pull2
include replicate_settings.txt
group nucl type <> 20 41
group dna type 41
group ps type 42
group dna_all union dna ps
group notdna subtract all dna_all
neigh_modify exclude molecule/intra nucl
neigh_modify exclude molecule/intra dna_all
neigh_modify exclude type 41 42
neigh_modify exclude type 41 41
fix 2 notdna langevin 300.0 300.0 1000.0 123 gjf vhalf
fix 1 notdna nve
fix 3 dna_all rigid/nve/small molecule
fix 4 dna langevin 300.0 300.0 1000.0 123 angmom 3.0
fix bl all balance 1000 1.0 rcb
#fix C all recenter INIT INIT INIT
timestep 0.1
run 1000
timestep 1.0
run 10000
timestep 10.0
run 1000
fix 2 notdna langevin 300.0 300.0 100000.0 123 gjf vhalf
fix 4 dna langevin 300.0 300.0 100000.0 123 angmom 3.0
run 100000