Hello everyone, I am preparing a protein–protein complex for steered molecular dynamics (SMD) simulations in GROMACS and need to orient the structure so that the pulling coordinate is aligned with the x-axis. My current plan is to:

1. Compute the center of mass (COM) of each protein.
2. Define the vector connecting the two COMs.
3. Rotate the structure so that this vector aligns with the x-axis.
4. Use that orientation as the pulling direction in SMD.

I read several papers but none of them have explicitly mentioned which tool they used in the orientation. A simple search suggested me to use MDAnalysis, a python package. However, I am wondering if there are other tools that are commonly used or more robust for this task.