ainteratomic distances -- atoms too close?

Dear all,

I am trying to equilibrate a polymer chain with following parameters:

units lj
atom_style angle
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 1 check yes
restart 1000 equilibration.restart
read_restart equilibration.restart.10000
reset_timestep 0
group all type 1
dump 1 all custom 1000 eq.dump.* id x y z ix iy iz
dump_modify 1 format “d .5f .5f .5f %d %d %d”
angle_style cosine
angle_coeff 1 0
pair_style soft 1.12246152962189
#pair_modify shift yes
pair_coeff 1 1 20
bond_style hybrid harmonic fene
bond_coeff 1 fene 30 1.5 1 1.0
bond_coeff 2 harmonic 1 1.0
special_bonds fene
fix 1 all nve
fix 2 all langevin 1.0 1.0 2.0 424242
thermo 1000
thermo_style custom step temp epair emol press pxx pyy pzz vol
timestep 0.012
run 10000

this code runs, but only in serial without dangerous builds. Also, when I check my .dump file in vmd, I notice that there are bonds with lengths beginning from 0.1 – I am surprised, because lammps does not crash or produce any warnings about this. Is this normal behaviour or is it dangerous? It seems to me that if I cannot run lammps in parallel with this code, something must be wrong with the configuration, however, I have checked that none of the atoms overlap initially.

thank you very much in advance for any input!


You could try running initially with fix nve/limit which
is a way to unoverlap since it doesn't let atoms move very far.
You are also not using pair_style soft the way it is intended,
which is to ramp the prefactor over time from very soft to
harder. If you do this slowly enough it is very effective at
unoverlapping systems.