if you're looking at the geometry of the box, make sure to do imaging on
your system first. look at the tutorials and also the Amber archives for
more details.
On Tue, Oct 27, 2015 at 8:44 AM, Andrew Bostick <andrew.bostick1.gmail.com>
wrote:
> Dear amber users,
>
> I did md simulation of my protein-ligand using ambertools14.
>
> After putting complex in a cubic box of water molecules, I saw the system
> (pdb file) using vmd. Also, after the equilibration step, I saw the
> trajectory using vmd. At first, I loaded prmtop file. Before loading mdcrd
> file, I determined amber coordinates with periodic box as file type.
> Unfortunately, in this trajectory, the cubic box was not seen and box is
> not cubic (it likes to sphere).
>
> please note the figure in the following link:
>
>
> https://www.dropbox.com/s/bc0v15jys449b7d/photo_2015-10-27_15-08-07.jpg?dl=0
>
> Is thers any problem in MD simulation?
>
> Any help will highly appreciated.
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Received on Tue Oct 27 2015 - 06:30:07 PDT
