Error while running NEB simulation for RIGID body simulation

Hi everyone,

I’m currently working on modeling NaO2. Oxygen atoms of superoxide ions are bonded and act like a RIGID 180-degree bond orientation. Sodium ions are treated as point masses. Additionally, I’ve introduced a massless particle at the center of mass (COM) of the superoxide ions. This modification is made to account for the buck potential parameters, as suggested in the literature. For a clearer understanding, you can refer to the input structure file attached below.

I’m trying to calculate rotational energy barrier for this system by rotating just one superoxide ion using NEB method. To do this, in a supercell of 1024 atoms (4x4x4), while keeping other atoms at same, I tried to change coordinates of a pair of oxygen atoms and massless COM particle (of a superoxide ion) in the final replica.
Following are my initial and final replicas, and input files.

But, I seem to getting: “ERROR: Incorrect atom format in NEB file (…/neb.cpp:454)
Last command: neb 0.0 0.1 1000 1000 100 final final_NaO2”

My final contains coord of one superoxide ion, since I wanted to find transition path of one superoxide ion. So can someone help me understand this error? I don’t see RIGID body based examples anywhere yet. So is that affecting the calculations here?

Thanks in advance!

final_NaO2 (318 Bytes)
initial_NaO2 (53.2 KB)
NaO2.neb (2.3 KB)

The error means that your final_NaO2 file has an incorrect file format. The format is described in the neb documentation. It is different from a data file that you are using.

You don’t see any examples for NEB with rigid bodies because it cannot be done. NEB invokes a minimizer and using fix rigid with minimization is not possible. Rigid body motions during minimization is a very, very tricky thing. So typically people would have to resolve to simulated annealing, which - in turn - is incompatible with NEB.

1 Like