2006-09-28 03:50:55 +08:00
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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thermo_style multi
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thermo 50
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2010-04-10 06:12:15 +08:00
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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2006-09-28 03:50:55 +08:00
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fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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group peptide type <= 12
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2012-01-13 03:03:12 +08:00
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#dump 1 peptide atom 10 dump.peptide
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#dump 1 peptide image 25 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 1 pad 3
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2010-01-15 05:38:16 +08:00
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2012-05-22 23:12:29 +08:00
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#compute bnd all property/local btype batom1 batom2
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2012-01-13 03:03:12 +08:00
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#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
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2006-09-28 03:50:55 +08:00
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run 300
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2007-10-06 01:53:44 +08:00
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