Problems with molecule topology in deposit

Dear all,

I’m new using LAMMPS and I’m interested in perform MD simulations of the deposition of molecules on metal surfaces. So first, I’m trying to adapt the in.deposit.molecule example given in the code for the water molecule that includes, at least, one term of angle, but the simulation stops with the error

ERROR: Molecule toplogy/atom exceeds system topology/atom.

Following the example and the manual instructions, I’ve defined 3 atom types in the create_box command: the first one for the metal atom and the other two for the oxygen and hydrogens of the water molecule. Also, I’ve setted the bond (O-H) and angle (O-H-O) types to 1, respectively, whose parameters are given in the main lammps input file (see attachment). However, I’m confusing about the extra terms. In my understanding, the extra/bond/per/atom should be equal to 2 since oxygen has two bonds with hydrogens, and extra/angle/per/atom should be equal to 1 which corresponds to the single angle, OHO. Is this the origin of the error or does it need to define also some extra special term for this case? If yes, how can I know the correct numbers for the water molecule? I’m using the LAMMPS version of 21 Oct 2014.

Please, could someone help me to understand and fix this error? I would be very gratefull for any help!

Follow below the molecule.water file and the main input file (attached) used in my tests:

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.5 on Sun Nov 16 21:44:47 BRST 2014
3 atoms
2 bonds
1 angles


1 -0.000000 -0.000000 0.397333 # OW H2O
2 -0.540000 0.540000 -0.198667 # HW H2O
3 0.540000 -0.540000 -0.198667 # HW H2O


1 2
2 3
3 3


1 -0.834000
2 0.417000
3 0.417000


1 1 1 2
2 1 1 3


1 1 2 1 3

Special Bond Counts

1 2 0 0
2 1 1 0
3 1 1 0

Special Bonds

1 2 3
2 1 3
3 1 2

Thanks & All the best,

Max Pinheiro Jr (1.77 KB)

Dear all,

I tried to send a mesage to the LAMMPS mailing list but the body of the text was not acessible in the forum. I don’t know why. So I’m sending the mesage again and I hope it works know. I’m sorry, It’s my first post in this forum.

All the best

---------- Mensagem encaminhada ---------- (1.77 KB)

You do also need extra special per atom. For water
molecules, that would also need to be 2, since each
atom in the water will have 2 special neighbors (the
other 2 atoms in the molecule, which are within 3 hops