From: Ashar Malik (
Date: Tue May 29 2018 - 21:00:08 CDT

In my opinion there are two separate things here (depending on how you look
at it).

First is the periodic boundry. To remove the periodic boundry you would
have to know how the trajectory was made. E.g. you can use the pbc unwrap
for charmm/namd based trajectories. Similarly I believe the command is
trjconv in GROMACS for trajectories calculated by the same.

After this you will get trajectories which you can use the way you explain

Load trajectory into vmd and use RMSD trajectory tool, by first aligning
the molecule to remove translation and rotation and then calculating the

Hope this was helpful, otherwise write back.

On May 30, 2018 13:51, "Gulce Kalyoncu" <> wrote:

Hello Everyone,

I would like to remove rotational degrees of freedom of three particles in
vmd by using trajectory tool. However, the system that I am working on has
periodic boundaries and after alignment I have some points with coordinates
which are out of my imaginary box. Does anyone know a proper way to remove
the rotational degrees of freedom for such a system? I appreciate any help
that you can provide.

Best Regards,
Gulce Kalyoncu