Issue with bond atoms missing at proc 0 at step

Hello,

When I run the following in. file (at end of email), I always encounter an error “bond atoms i j missing at proc 0 at step x”. I’m following the parameter settings from this paper (https://www.biorxiv.org/content/10.1101/2020.05.12.091041v1.full.pdf). I’ve played with the neighbor bin size, I’m modifying neighborhoods as frequently as possible, defined a cutoff, and using small time steps. Basically, throwing everything I can find at it, and still there doesn’t seem to be a clear solution - inevitably the error occurs.

Additionally, if I cut the soft potential set up before any errors are returned (and I’ve tried at multiple time points to make sure it didn’t just coincidentally end when an error was about to occur) and switch to the equilibration setup, it immediately returns the error “bond atoms i j missing at proc 0 at step x”, regardless how many steps the soft potential is run for, and wondering why this might be.

Best,
Christian

in.chrom (I submitted another version of this in another post for a different question):

units lj
dimension 3
processors * * *
boundary f f f

neighbor 5.0 bin
neigh_modify every 1 delay 0
timestep 0.00001

atom_style hybrid angle ellipsoid
read_data data.chrom
special_bonds fene

##SOFT POTENTIAL###

pair_style soft 1.12246
pair_coeff * * 1.0 1.12246

bond_style fene
bond_coeff 1 30 1.6 0 0

comm_modify cutoff 6.5

angle_style cosine/periodic
angle_coeff 1 3 -1 1

velocity all create 1.0 2349852
thermo 250
dump 2 all custom 100 md.lammpstrj id type x y z
fix 1 all nve/dotc/langevin 1.0 1.0 100.0 100 angmom 10
run 8750

###EQUILIBRATE####
pair_style lj/cut 1.12246
pair_coeff 1 1 1 1.0 1.12246
pair_coeff 1 2 1 1.0 1.12246
pair_coeff 1 3 1 1.0 1.12246
pair_coeff 2 2 1 1.0 1.12246
pair_coeff 2 3 1 1.0 1.12246
pair_coeff 3 3 1 1.0 1.12246
pair_coeff 4 4 1 1.0 1.12246
pair_coeff 3 4 1 1.0 1.12246
pair_coeff 2 4 1 1.0 1.12246
pair_coeff 1 4 1 1.0 1.12246
pair_modify shift yes

reset_timestep 0

run 2000000

you still don’t report your LAMMPS version and platform.
for future reference, please read this: https://lammps.sandia.gov/guidelines.html

have you visualized your simulation? that is the first thing to do when unexpected things happen.

you have fixed boundaries and there appear to be no wall potentials or immobile atoms blocking atoms from leaving the box.
as soon as an atom has left the box it will be removed from the system at the next neighbor list update.
if that atom is part of a bond, you get the error message you see.

axel.