53 lines
1.4 KiB
Plaintext
53 lines
1.4 KiB
Plaintext
# solvated ubiquitin molecule with AMOEBA force field
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units real
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boundary p p p
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atom_modify sort 0 0.0
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atom_style amoeba
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bond_style class2
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angle_style amoeba
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dihedral_style fourier
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improper_style amoeba
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# per-atom properties required by AMOEBA or HIPPO
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fix amtype all property/atom i_amtype ghost yes
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fix extra all property/atom i_amgroup d_redID d_pval ghost yes
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fix extra2 all property/atom i_polaxe d2_xyzaxis 3
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fix pit all amoeba/pitorsion
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fix_modify pit energy yes
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fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
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fix_modify bit energy yes
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# read data file
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read_data data.ubiquitin fix amtype NULL "Tinker Types" &
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fix pit "pitorsion types" "PiTorsion Coeffs" &
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fix pit pitorsions PiTorsions &
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fix bit bitorsions BiTorsions
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pair_style amoeba
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pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
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special_bonds lj/coul 0.5 0.5 0.5 one/five yes
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# thermo output
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compute virial all pressure NULL virial
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thermo_style custom step temp epair ebond eangle edihed eimp &
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emol etotal press c_virial[*]
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#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
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#dump_modify 1 sort id
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# dynamics
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fix 1 all nve
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thermo 1
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run 10
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