34 lines
712 B
Plaintext
34 lines
712 B
Plaintext
units lj
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dimension 3
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boundary f f p
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pair_style lj/cut 1.1225
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read_data thylakoid.data
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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# Makes about 100 particles type 2:
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region make_two sphere -29 0 0 6.25
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region everywhere block -25 25 -25 25 -25 25
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group two region make_two
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set group two type 2
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# And deletes some of type 1 to allow more movement:
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group one type 1
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set group one type 1
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delete_atoms porosity everywhere 0.2 123
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# Start run
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variable wB equal 5.0
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variable LB equal 10.0
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variable lB equal 3.0
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fix step all nve/manifold/rattle 1e-4 10 thylakoid ${wB} ${LB} ${lB}
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thermo_style custom time step pe ke etotal temp
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thermo 2500
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dump traj all custom 10000 thylakoid.dump id type x y z
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run 25000000
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