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