ERROR on proc 0: Bond atoms 7626 7627 missing on proc 0 at step 40

I’m trying to execute a script to relax the system of buckypapers and then using the output for the tensile test, but I’m getting this error when my timestep is 0.01:
ERROR on proc 0: Bond atoms 7626 7627 missing on proc 0 at step 40
It gives output for only step 0.

When I increased the timestep to 0.01, I got the following output till step 20000 (i.e, nan for every variable)
Per MPI rank memory allocation (min/avg/max) = 10.8 | 10.8 | 10.8 Mbytes
Step TotEng KinEng PotEng E_vdwl E_mol E_bond E_angle Temp c_mytemp Lx Ly Lz CPU Press Pxx Pyy Pxy
0 70664993 0 70664993 -181855.72 70846849 70498101 348747.72 0 0 1218.6026 712.02437 90.5552 0 -1186989.7 -1794579.7 -1737326.9 -1615.2118
1000 nan nan nan 0 nan nan nan nan nan nan nan 90.5552 1.926088 nan nan nan nan
2000 nan nan nan 0 nan nan nan nan nan nan nan 90.5552 3.952089 nan nan nan nan

I can’t share the input file as I’m a new user, but I’ll copy-paste it in the thread if required to solve the problem.

Thank You!

Please post LAMMPS issues in the LAMMPS Category instead of under the Materials Project Category. I will move your topic over this time.

Look at your energies. They are insanely high, especially for bonds and angles. That means something is wrong with your topology, your geometry, or with your data file or a combination of those.

How can I share data file and input script, so that you can have look into it because previously I was able to simulate on this data using “real” units but now I have changed it to “metal” units. Also i have changed boundary conditions from p p s to p p p?
Does that affect the output?

Create a tiny data file with just a small number of atoms that shows the same issue.
Since you seem to be new to this, it is a bad idea anyway to start with large system simulations. You will make mistakes and with a large system you just have to wait much longer. But if you figure out the procedure with a “toy system”, you will learn how to debug your inputs and find good simulation settings for dependable results much more quickly. Also it is much easier to manually validate your files.
I have just demonstrated to you how to do this with the reply here:

You can provide access to larger files by uploading them to dropbox, onedrive, google drive or similar and then providing a link. But don’t get your hopes up. I will not look at large files or check inputs that need a long time to run. I don’t have the time for that and it is not necessary, anyway (see my comments above).

Please note that a simulation that completes does not automatically mean that it is correct. It just means that you did not have any drastic events happening that lead to invalid data or atoms being propelled across the system too fast.

You can see from the discussion of units units command — LAMMPS documentation
what changes when changing units. For metal vs. real, the length unit is the same, but e.g. energy, time, pressure (and derived properties) are different.

Changing the boundary conditions can make a difference when you have non-zero image flags or bonds that now cross the box but previously were between periodic cells. Only a careful check of the data file can tell if that makes a difference in your specific case.