45 lines
1.0 KiB
Plaintext
45 lines
1.0 KiB
Plaintext
# 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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group peptide type <= 12
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group one id 2 4 5 6
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group two id 80 82 83 84
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group ref id 37
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group colvar union one two ref
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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fix 2 all plumed plumedfile plumed-restraint.dat outfile p.log
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fix 2a ref setforce 0.0 0.0 0.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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dump dd all xyz 10 lammps.xyz
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variable step equal step
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variable pe equal pe
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fix 5 all print 10 "$(v_step) $(v_pe)" file lammps_energy
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dump mq all custom 200 mq_lammps id mass q
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run 101
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