package omp 8
units real
boundary p p p
atom_style full
read_data data.TTA
# interaction styles
# pair_styles documentation page: http://lammps.sandia.gov/doc/pair_lj.html
pair_style lj/cut/coul/long 0.2 9.0
kspace_style ewald 1.0e-4
# I'm only testing with coul/long right now to make sure I'm not getting errors from coul/dsf. I'd like to use coul/dsf eventually:
# pair_style lj/cut/coul/dsf 0.2 9.0 12.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style harmonic
pair_modify mix geometric tail no
# OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
# force field parameters
# missing nonbonded parameters are inferred from mixing.
#field, atom type, atom type, eps(kcal/mol), sigma(angstroms) [http://lammps.sandia.gov/doc/pair_coeff.html]
pair_coeff 1 1 0.1050 3.7500 # C
pair_coeff 2 2 0.0660 3.5000 # CT
pair_coeff 3 3 0.2100 3.3000 # CZ
pair_coeff 4 4 0.0300 2.5000 # HC
pair_coeff 5 5 0.0000 0.0000 # HO
pair_coeff 6 6 0.2100 2.9600 # O
pair_coeff 7 7 0.1700 3.0000 # OH
#field, bond type, kb, r0 [http://lammps.sandia.gov/doc/bond_coeff.html]
bond_coeff 1 400.00 1.4440 # C-CZ
bond_coeff 2 570.00 1.2290 # C-O
bond_coeff 3 450.00 1.3640 # C-OH
bond_coeff 4 390.00 1.4700 # CT-CZ
bond_coeff 5 340.00 1.0900 # CT-HC
bond_coeff 6 1150.0 1.2100 # CZ-CZ
bond_coeff 7 553.00 0.9450 # OH-HO
#field, angle type, kb, theta0 [http://lammps.sandia.gov/doc/bond_coeff.html]
angle_coeff 1 150.0 180.00 # C-CZ-CZ
angle_coeff 2 35.0 113.0 # C-OH-HO
angle_coeff 3 150.0 180.0 # CT-CZ-CZ
angle_coeff 4 80.0 120.4 # CZ-C-O
angle_coeff 5 70.0 108.0 # CZ-C-OH
angle_coeff 6 35.0 108.5 # CZ-CT-HC
angle_coeff 7 33.0 107.8 # HC-CT-HC
angle_coeff 8 80.0 121.0 # O-C-OH
#field, dihedral type, K1, K2, K3, K4 [http://lammps.sandia.gov/doc/dihedral_coeff.html]
dihedral_coeff 1 0.0 0.0 0.0 0.0 # CT-CZ-CZ-C
dihedral_coeff 2 1.5 5.5 0.0 0.0 # CZ-C-OH-HO
dihedral_coeff 3 0.0 0.0 0.0 0.0 # HC-CT-CZ-CZ
dihedral_coeff 4 0.0 0.0 0.0 0.0 # CZ-CZ-C-O
dihedral_coeff 5 0.0 5.0 0.0 0.0 # O-C-OH-HO
dihedral_coeff 6 0.0 0.0 0.0 0.0 # CZ-CZ-C-OH
#field, improper type, K1, X0 [http://lammps.sandia.gov/doc/improper_coeff.html]
improper_coeff 1 7.000 180.0
run_style verlet #The verlet style is a standard velocity-Verlet integrator.
# velocity command documentation: http://lammps.sandia.gov/doc/velocity.html
velocity all create 300.0 239847 dist gaussian mom no rot no
# fix command documentation: http://lammps.sandia.gov/doc/fix.html
fix 1 all nve
dump 98 all xyz 100 TTA-start.xyz
# run just a few steps to get rid of all the symmetry
run 100
# minimize command documentation: http://lammps.sandia.gov/doc/minimize.html
minimize 1.0e-5 1.0e-6 10000 100000
# Write a restart file after minimization, which can be picked up and used as a checkpoint later if necessary
write_restart TTA-min.restart
dump 99 all xyz 100 TTA-min.xyz
# Optional, as far as I can tell: change the timestep to a smaller value. LAMMPS real units are femtoseconds.
timestep 0.25 #resets timestep to 0.25 fs
reset_timestep 0 #does not reset the timestep between force calculations, but changes the counter to 0. Do this after minimization
# neigh_modify command documentation: http://lammps.sandia.gov/doc/neigh_modify.html
neigh_modify every 10 delay 20 check yes
thermo 200 #compute and print thermodynamic information every 200 timesteps.
thermo_style multi #prints a multiple-line summary of information. Can also use "one" or "custom ___" where ___ is other arguments
velocity all scale 300 #scales all particle velocities to accomplish a temperature of 300 K
# fix langevin documentation: http://lammps.sandia.gov/doc/fix_langevin.html
# fix 2 all langevin 300.0 300.0 50.0 6243
# fix nvt command documentation: http://lammps.sandia.gov/doc/fix_nh.html
fix 2 all nvt temp 300.0 300.0 100.0
# dump command documentation: http://lammps.sandia.gov/doc/dump.html
dump 1 all dcd 4 TTA-eq.dcd
# dump_modify command documentation: http://lammps.sandia.gov/doc/dump_modify.html
dump_modify 1 unwrap yes
run 5000
#save a restart file of this as well
write_restart TTA-eq.restart