Hello all,
With some insight from Steve regarding the langevin thermostat I was able to simulate rigid molecules in bulk and
obtain acceptable MSD values. I am currently trying to simulate rigid dumbbell molecules in confinement. With 2 fcc wall
structures, containing atoms with a fixed positions in the z axis. The atoms that consist of the wall have a zero velocity
and a set force of zero. In this case the thermostat reduces the temperature to approx T* = 1.3 instead of T* = 2. Also I
would like to point out the MSD values calculated from lammps are very large in comparison to the m.d code. Any insight in
working with confinement and would be of tremendous values. Sincerely
Ravi
# 3d confinement simulation
units lj
atom_style molecular
dimension 3d
boundary p p f
read_data data.ljconfine
mass 1 1.0
mass 2 1.0
mass 3 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 1 2 1.0 1.0
pair_coeff 1 3 1.0 1.0
pair_coeff 2 2 1.0 1.0
pair_coeff 2 3 1.0 1.0
pair_coeff 3 3 0.0 0.0
group wallupper type 3
group dumbbell molecule <> 1 200
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 wallupper setforce 0.0 0.0 0.0
fix 2 dumbbell rigid molecule
fix 3 all langevin 2.0 2.0 500.0 48279
dump 1 dumbbell xyz 100 dump.xyz
thermo 100
run 60000
run_style verlet
timestep 0.005