Hi,
I wish to setup a wall with atoms vibrating about their mean positions constrained by a fene potential. For the same I am creating a molecule of 2 atoms, connected by a fene bond and keeping one atom frozen at the expected mean position. To avoid any other pair potential interaction I am setting pair_coeff 1 2 0.0 0.0. But upon simulating, the program gives warnings that FENE bond too long. I am unable to find out the reason for this, as the atoms are interacting only through the FENE potential and there should be no reason that they are repelled out so far. My input file is as follows. I would be extremely thankful if somebody can point me to the idea I might be missing out here.
3-d LJ flow simulation
units lj
dimension 3
newton on
processors 2 2 1
boundary p p p
atom_style bond
create geometry
read_data data.Capillary
special_bonds fene
bond_style fene
bond_coeff 1 30 1.5 0.0 0.0
define groups
group fix type 1 # frozen atom
group mobile type 2 #mobile atom
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
neigh_modify exclude group fix fix check no #exclude all interactions between frozen atoms
LJ potentials
pair_style lj/cut 2.5
pair_coeff 1 1 0.0 0.0
pair_coeff 1 2 0.0 0.0
pair_coeff 2 2 0.8 0.6
initial velocities
communicate single vel yes
velocity mobile create 1.0 1290
velocity fix create 0.0 1290
fix 1 mobile nvt 1.0 1.0 100.0
fix 2 fix setforce 0.0 0.0 0.0
Run
timestep 0.00144
run_style verlet
thermo 100
reset_timestep 0
dump 1 all xyz 500 Capillary.xyz
run 10000
With regards,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA