VMD-L Mailing List

From: SHIVAM TIWARI (t.shivam_at_iitg.ac.in)
Date: Wed Jun 26 2024 - 03:30:19 CDT

Dear all,

Is it possible to wrap atoms along a specific axis using pbctools in vmd? For example, I want to wrap a set of atoms which are leaving the simulation box from X or Y direction and let the coordinates of atoms which leave the box from Z direction be unwrapped.

something like this: pbc wrap -center com -sel "ions" -axis "X or Y" -compound residue

I know there is no option as "-axis", but is there a workaround which could achieve this.

regards,
SHIVAM