Error on bond atoms missing (ntopo-bond partial)

Hi Dear
my simulation has 3 material as oil-water and calcite, oil and water has beend relaxed and minimized individually and unwrapped in z direction and are placed in z direction in parallel way.
(files has been attached) but with running in nvt ensemble in about 500 femtosec error ( bond atom missing on proc 0 ntopo_bond partial ) appears and simulation stopped.
where is the problem?
thank you (8.8 MB) (6.7 KB)

We already discussed that your way of setting up such a system is less than ideal. This is a major contributing factor.

The direct cause are atoms moving too fast. If that happens during the early stages of a simulation that often means that they have high potential energy due to close contacts. Other potential causes: wrong choice of force field parmaters (i.e. incorrect atom type assignment), mixing of incompatible force fields, bad molecular topology, bad simulation parameters (e.g. too large time step) and a bunch more.

The fact that you have a crazy high pressure at the beginning yet very negative energy is not a good sign and often caused by a bad geometry or box dimensions.

Finally, the fact that you are using a hybrid lj/cut/coul/long lj/cut pair style is reason for concern. a) no hybrid should be needed since lj/cut/coul/long includes lj/cut and kspace always operates on all atoms, so all atoms should have a suitable charge (or set to 0) and the pair style should compute the resulting forces. But this also hints at you combining two force fields that use a very different parameterization philosophy and thus should not be combined.

There are also errors in the input. Have you noticed this warning?

WARNING: One or more atoms are time integrated more than once (src/modify.cpp:289)

That should not be ignored for your kind of system.

Talking of time integration, please not that fix rigid is not applied during minimization. But then again, if you want to immobilize atoms, just don’t apply time integration to those atoms at all.

final (8.2 KB) (5.5 MB)
thanks dear axel
in other approach, 3 materials(calcite-oil-water) that calcite is surface and oil is on the calcite in z direction, equilibrated water is on the oil too. in this materials only water is relaxed. these materials are merged together by first input file and mix file created. after that, final input is running with mix file to start simulation but this error display : ERROR on proc 0: Bond atoms 1380 1387 missing on proc 0 at step 872 (…/ntopo_bond_all.cpp:63)
Last command: run 100000

what went wrong
thanks (665.4 KB)
first (6.9 KB) (1.6 MB) (2.9 MB)

Same thing as before.