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!
A