units real
boundary p p p
atom_style full

read_data data.glycine-test

# interaction styles
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-6
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style harmonic
pair_modify mix geometric tail yes


# 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 # C1
pair_coeff   2 2   0.0660   3.5000 # C2
pair_coeff   3 3   0.0000   0.0000 # H1
pair_coeff   4 4   0.0300   2.5000 # H2
pair_coeff   5 5   0.0000   0.0000 # HW
pair_coeff   6 6   0.1700   3.2500 # N
pair_coeff   7 7   0.2100   2.9600 # O1
pair_coeff   8 8   0.2100   2.9600 # O2
pair_coeff   9 9   0.1521   3.15061 #OW

bond_coeff   1      434.00 1.0100 # H1-N
bond_coeff   2      367.00 1.4710 # C2-N
bond_coeff   3      340.00 1.0900 # C2-H2
bond_coeff   4      656.00 1.2500 #  C1-O1
bond_coeff   5      600.00 0.9572 # HW-OW
bond_coeff   6      656.00 1.2500 #  C1-O2
bond_coeff   7      317.00 1.5220 # C1-C2

angle_coeff  1      70.00 117.00 #  C2-C1-O2
angle_coeff  2      80.0  111.2  # C1-C2-N
angle_coeff  3      35.0  109.5  #  C1-C2-H2
angle_coeff  4      75.0  104.52 #  HW-OW-HW
angle_coeff  5      35.0  109.5  #  H1-N-H1
angle_coeff  6      35.0  109.5  # C2-N-H1
angle_coeff  7      35.0  109.50  #  H2-C2-N
angle_coeff  8      33.0  107.80  # H2-C2-H2
angle_coeff  9      80.0  126.0  # O1-C1-O1
angle_coeff  10     70.00 117.00 #  C2-C1-O1


dihedral_coeff  1    0.000  0.000  0.300  0.000 # H2-C2-N-H1
dihedral_coeff  2    0.000  0.820  0.000  0.000 #  O-C1-C2-N
dihedral_coeff  3    0.000  0.000  0.000  0.000 # O-C1-C2-H2
dihedral_coeff  4    0.000  0.000  0.347  0.000 # C1-C2-N-H1
dihedral_coeff  5    0.000  0.820  0.000  0.000 #  O-C1-C2-N
dihedral_coeff  6    0.000  0.000  0.000  0.000 # O-C1-C2-H2


improper_coeff  1    21.000 180.0  #C2-O-C1-O

#minimize
minimize 1.0e-4 1.0e-6 10000 100000


run_style verlet 
reset_timestep 0 
timestep 2.0
velocity all create 270.0 239847 

fix 1 all nve
fix 2 all langevin 270.0 270.0 2000.0 699483
fix 3 all shake 0.000001 20 100000 b 1 3 5 a 4 
fix 4 all press/berendsen iso 1.0 1.0 1000000.0

#fix 1 all npt temp 270.0 270.0 100.0 iso 1.0 1.0 1000.0

neigh_modify every 1 delay 0 check yes
neighbor 2.0 bin


thermo 1 
thermo_style multi 



dump 3 all dcd 1000 glycine_water.dcd
dump_modify 3 unwrap yes
#dump 4 all custom 5 dump.force.* id fx fy fz
#dump 5 all custom 5 dump.posit.* id x y z vx vy vz
run 10000