VMD-L Mailing List

From: quantrum75 (quantrum75_at_yahoo.com)
Date: Mon Nov 15 2010 - 15:26:18 CST

Hi VMD users,
I am running a protein simulation using gromacs. I have an xtc trajectory from GMX. When I visualize the trajectory in VMD, I set the water representation to be within 5 A of the protein. When I visualize the simulation, I see that the water molecules expand in the simulation since I believe the initial set of water molecules are tracked for the entirety of the simulation and once they go beyond the 5 A, they are still tracked in VMD (in the representation). Is there anyway I can set a PBC like setup so that only the molecules within 5 A of the protein are visualized in VMD and once they go beyond 5 A dissappear?
I am sure this question was asked before, I honestly tried hard to find that particular thread without success. I would grateful if someone could point me to it. If not, is there a way to do it?
Thanks!
Rama
--- On Mon, 11/15/10, David Wedner <wedner.david_at_yahoo.com> wrote:

> From: David Wedner <wedner.david_at_yahoo.com>
> Subject: vmd-l: Measure Radius of gyration
> To: vmd-l_at_ks.uiuc.edu
> Date: Monday, November 15, 2010, 1:31 PM
> Hi,
> I want to measure the radius of gyration of some methane
> molecules in a cubic water box
> the problem is that due to the applied periodic boundary
> conditions some molecules are transformed to the other side
> of the box
>
> how to transfer these molecules back to their parent
> position so that I have all molecules together ?
>
> Thanks
>
> David
>
>
>
>