Hi all,
I am trying to run an equilibrium MD simulation of polymers using LAMMPS. I had previously run these simulations on HOOMD and want to now run them on LAMMPS. I first want to reproduce the runs done on HOOMD in LAMMPS.
The polymers have 50 Lennard Jones beads connected by harmonic bonds. The MD simulation is run at a reduced temperature of 1.7 and reduced density of 0.8. At this temperature and density, the polymers are reported to be in a homogeneous dense phase. The initial configuration of polymers is taken from an equilibrated trajectory of the polymers obtained using HOOMD. While the equilibrium MD run at the given density and temperature generates a homogeneous dense phase in HOOMD, the LAMMPS run generates a slab.
Below is my LAMMPS input file:
variable t equal 1.7
units lj
atom_style molecular
dimension 3
boundary p p p
#read input configuration
read_data polymer.data
#all particles has mass 1
mass * 1
#Harmonic type bond here k is actually k/2
bond_style harmonic
bond_coeff * 37500.0 1.0
velocity all create $t 87287 loop geom
timestep 0.001
#computes a truncated and force-shifted LJ interaction (aka Shifted Force Lennard-Jones)
pair_style lj/smooth/linear 6.0
pair_coeff * * 1.0 1.0
#neighbor 2.0 bin
#neigh_modify delay 0 every 1 check yes
minimize 0.0 1.0e-8 1000 100000
fix 1 all nvt temp $t $t 1.0
dump mydmp all atom 5000 dump.emd.0.8.lammpstrj
thermo_style custom step time temp press pe lx ly lz density
equilibration run
thermo 1000
run 500000
Can you please help in finding out why LAMMPS simulation does not generate a homogeneous phase at T=1.7 for a density of 0.8 while MD run of the polymers in HOOMD at same conditions generates a homogeneous phase?
Thanks in advance.