VMD-L Mailing List

From: quantrum75 (quantrum75_at_yahoo.com)
Date: Mon Nov 15 2010 - 17:14:39 CST

Dang!
Now I remember where I read it!...It was in the manual! sorry for the post! Thanks Josh and Axel. I promise to look a bit more carefully next time.
Regards
Rama

--- On Mon, 11/15/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Subject: Re: vmd-l: Water molecules within a definite radius
To: "quantrum75" <quantrum75_at_yahoo.com>
Cc: vmd-l_at_ks.uiuc.edu
Date: Monday, November 15, 2010, 5:22 PM

On Mon, Nov 15, 2010 at 4:26 PM, quantrum75 <quantrum75_at_yahoo.com> wrote:
> 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?

all you have to do is to read the documentation!

the selection criterion is applied only once, unless
you activate "Update Selection Every Frame" in the
'Trajectory' tab of your representation.

axel.

> 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
>>
>>
>>
>>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.