VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Sun Oct 07 2018 - 12:06:37 CDT

VMD units are in Angstrom so this is the box size in A and angles of the box

On Sun, Oct 7, 2018 at 5:09 PM Mayank <fireball4556_at_gmail.com> wrote:

> I am doing a simulation on liquid argon and using PBC(default in gromacs)
> on it. When I load the trajectory in vmd and construct a box using `pbc
> box` it is a constant for my simulation.
> Now, I want to calculate the dimensions of this box.
> I tried using `pbc get -now` and got this:
> {77.394997 77.394997 77.394997 90.000000 90.000000 90.000000}
>
> I dont understand what are these the coordinates of, especially because
> when i open the coordinates files it has values ranging from 0 to
> approximately 8 nm.
>
> Can someone explain this output or how to obtain the dimension of my PBC
> box ?
>
> Regards,
> Mayank
>