VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Mon Nov 15 2010 - 17:06:05 CST

Hi Rama,

Simple fix -- under the 'selections' tab on the 'representations' palette, select the option for 'update selection every frame'. I think that should give you want you want.

Josh

On Nov 15, 2010, at 4:26 PM, quantrum75 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?
> 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
>>
>>
>>
>>
>
>
>