Bond atoms missing in adsorption

LAMMPS LAMMPS General Discussion
1

Dear all

I am attempting to simulate water adsorption on MOF and have encountered the following error:

Bond atoms 3926 3928 missing on proc 9 at step 1768

lammps version : LAMMPS (7 Feb 2024 - Update 1)

In my simulation, I first read the MOF structure and create water atoms inside the box.

Here I tried flexible water model using spc/fw water and mSPC/fw (DOI: 10.1039/c6cp06770k), one uses harmonic bonds and another one uses morse bonds for bond streching.

For the pure water, both 2 water models can work.

However, the adsorption simulation can run smoothly with harmonic bond, but it always shows ‘bond atom missing’ with morse bonds.

I read from here [lammps-users] ERROR on proc: Bond atoms missing and here Problem with bond or angle atom missing that the possible reason might be

  1. reneighboring far too infrequently: I reneighbor every 1 step.
  2. large time step: I tried 0.1 fs and 0.25 fs, they works for harmonic bond but not morse bond.
  3. some atoms overlap: I tried delete_atoms overlap 0.5

It will be highly appreciated if someone could give me some suggestion about how to handle this.

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Warnings I’ve got:

1. WARNING: Triclinic box skew is large. LAMMPS will run inefficiently.

As I am doing only NVT and NVE simulation, the box will not change, so this will not cause big problem.

2. WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies

This may be caused by using

neigh_modify 	exclude group frame frame check no

But this is to exclude the intra framework interactions as we consider it rigid.

3. WARNING: Ignoring 'compress yes' for molecular system

‘compress yes’ is not done for molecular systems (see the atom_style command), regardless of the compress setting. So this warning can be no trouble.

Below are my input files.

data.MIL-101-primitive (1.4 MB)
FlexibleH2O.txt (370 Bytes)
in.mspcfw.lammps (4.4 KB)
in.spcfw.lammps (4.5 KB)

Thanks
JIANG

2

You missed out on the most common reason for this error: bad force field parameters.
With the Morse potential bonds can break and that would be disastrous in your setup, since there is no provision for reactions or a proper adjustment of the charges. So if something pulls on the bonds too much, you get the error. With harmonic bonds, this is not possible, since the potential keeps pulling back the atoms to the bond.