forked from lijiext/lammps
42 lines
849 B
Plaintext
42 lines
849 B
Plaintext
# Solvated 5-mer peptide
|
|
|
|
units real
|
|
atom_style full
|
|
|
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
bond_style harmonic
|
|
angle_style charmm
|
|
dihedral_style charmm
|
|
improper_style harmonic
|
|
kspace_style pppm 0.0001
|
|
|
|
read_data data.peptide
|
|
|
|
neighbor 2.0 bin
|
|
neigh_modify delay 5
|
|
|
|
timestep 2.0
|
|
|
|
group peptide type <= 12
|
|
group one id 2 4 5 6
|
|
group two id 80 82 83 84
|
|
group ref id 37
|
|
group colvar union one two ref
|
|
|
|
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
|
|
|
fix 2 all plumed plumedfile plumed.dat outfile p.log
|
|
fix 2a ref setforce 0.0 0.0 0.0
|
|
|
|
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
|
|
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
|
#dump_modify 1 sort id
|
|
|
|
thermo_style custom step temp etotal pe ke epair ebond f_2
|
|
thermo 10
|
|
variable step equal step
|
|
variable pe equal pe
|
|
|
|
run 101
|