Hi all,

I'm currently working with a simulation in VMD where my system's box starts from negative coordinates (e.g., x = -0.5, y = -0.5, z = -10.5) instead of starting at zero. I'm trying to apply periodic boundary conditions (PBC) using the pbc set command, but I’m encountering issues because the box is not aligned with the origin ( we can only use length in this command and the default origin is (0 0 0).

Can anyone provide guidance on how to correctly shift the box and apply periodic boundary conditions in VMD for a box starting from negative coordinates?

Thanks in advance for any help!