VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Sun Oct 07 2018 - 12:40:21 CDT

Hi Mayank,

Sounds like it is mostly units. VMD always gives distances/lengths in
angstrom, so 77.394 is basically 7.74 nm, which sounds about right for your
coordinates.

Hope this helps,
Chitrak.

On Sun, Oct 7, 2018 at 8:33 AM 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
>