problem with compute com/molecule gyration/molecule

Hello LAMMPS users:

I have some problems with the results of compute com/molecule and compute gyration/molecule.

I have a cluster of atoms (they have the same molecule tag) and as you can see in the attached snapshot, they are partitioned into 4 pieces by the periodic boundaries. When I used compute com/molecule and compute gyration/molecule to calculate the group’s center-of-mass (COM) and radius of gyration (Rg), the results seemed unreasonable. COM was in the middle of 4 separated pieces rather than inside the molecule. As a result, Rg was much larger than it should be.

I hope I clearly stated my problem. Any idea of something I did wrong? Thanks very much.

Shaorui
111.png

Hello LAMMPS users:

I have some problems with the results of compute com/molecule and compute gyration/molecule.

I have a cluster of atoms (they have the same molecule tag) and as you can see in the attached snapshot, they are partitioned into 4 pieces by the periodic boundaries. When I used compute com/molecule and compute gyration/molecule to calculate the group's center-of-mass (COM) and radius of gyration (Rg), the results seemed unreasonable. COM was in the middle of 4 separated pieces rather than inside the molecule. As a result, Rg was much larger than it should be.

I hope I clearly stated my problem. Any idea of something I did wrong? Thanks very much.

both computes are dependent on your initial configuration having
correct image flags set.

have you checked the original data file? can you write out a restart
and convert it with restart2data and check it?

axel.