Dear Axel and Shafat,

Thank you for the reply.

I add a command “delete_atoms overlap 1.0 all all” and get a answer as shown in picture below. Then, “-nan” error always occurs. I used PACKMOL package and used a distance cutoff of 2.0 Å between each atom to avoid any unrealistic overlap. Could you please give me advices How to configure initial geometry?

I appreciate any advices.

Thanking you for your time and advices.

Wu Minbo


The delete_atoms command was not meant to “fix” your bad input geometry, but merely to demonstrate that it has problems.
Please note, that close contacts can also arise through periodic boundaries from incorrectly specifying box boundaries.