Hello,
I am having trouble getting one of my programs to run and was wondering if you could help. I am fairly new to using LAMMPS, however I have gone thorough the manual, mail archives, and tutorials and I still cannot figure out my problem. The error I get is:
ERROR on proc 0: Bond atoms 72 73 missing on proc 0 at step 11248 (…/ntopo_bond_all.cpp:63)
I know in general what this error means and I know my input file is good. What happens at this step is that the Energy increases extremely and in VMD, I see some of the same atom type squished together. After trying many manipulations of my code, I still can’t find the problem. Are there any blatant problems you see that I do not?
#epsilon = 0.25KbT
#Sigma = 4.25e-10 m
thermo_modify flush yes
log ./logg.lammps append #keeps adding to the file
units lj
dimension 3
atom_style hybrid angle charge #bead-spring polymers with stiffness Polycat ID = 1
atom_style hybrid angle charge #NEUTRAL ID = 2
atom_style hybrid angle charge #Polyanions ID=3
atom_style hybrid angle charge #Cations ID=4
atom_style hybrid angle charge #Anions ID=5
bond_style class2
angle_style charmm
read_data ./AAA1lammpy.txt
neighbor 0.3 bin
neigh_modify every 1 delay 1 one 3000
pair_style hybrid/overlay lj/cut/coul/long 2.5 10 lj/cut 2.5
kspace_style pppm 1.0e-3
bond_coeff 1 1.05 1000 0 0
angle_coeff 1 $(4*1.679991641) 180 0 0
pair_coeff 1 1 lj/cut 43.0 1.0 1.0
pair_coeff 1 2 lj/cut 43.0 0.625 0.625
pair_coeff 1 3 lj/cut 43.0 1.0 1.0
pair_coeff 1 3 lj/cut/coul/long 43.0 1.0 1.0
pair_coeff 1 4* lj/cut/coul/long 43.0 1.0 1.0
pair_coeff 2 2 lj/cut 43.0 0.25 0.25
pair_coeff 2 3* lj/cut 43.0 0.625 0.625
pair_coeff 3 3 lj/cut 43.0 1.0 1.0
pair_coeff 3* 4* lj/cut/coul/long 43.0 1.0 1.0
dielectric 78.5
fix 1 all nve
fix 2 all langevin 4.0 4.0 1.0 1234
thermo 5000
timestep 0.0025
dump d1 all xyz 5000 ./myDumpAAAfixing.xyz
dump_modify d1 element O N K S H
run 5000000
echo log
run_style verlet
write_restart ./last.frame.*
To clarify, the pollination has both charged and uncharged atoms, with the uncharged atoms being a different size than the rest.
Thank you for your help.
Natalia