VMD-L Mailing List

From: Karteek Kumar (karthik3327_at_gmail.com)
Date: Mon Mar 28 2016 - 01:15:55 CDT

Hi Abhishek,

1) To create a box with dimensions x,y and z. use " pbc set { x y z } -all
"

-all is used for multiple frames.

2) To visualize the box " pbc box -center origin "

3) To wrap all the polymer chains

     pbc wrap -center origin -compound res ( molecular pbc)

     pbc wrap -center origin ( atomic pbc)

Hope this helps !!!

Thanks
Karteek

On Mon, Mar 28, 2016 at 11:20 AM, ABHISHEK GUPTA <akgiitm_at_gmail.com> wrote:

> Dear VMD users,
>
> I want to visualize my polymer chains in a cubic simulation box in VMD.
> How to create a cubic simulation box in VMD of given cubic side length ?
> DO i need a fortran code to do that ?
> How to put my chains inside this cubic simulation box ?
>
> Please help me with necessary procedure to do this task.
>
> Best regards
> Abhishek Gupta
>