From: Pat Yee (
Date: Mon Nov 15 2010 - 17:47:29 CST


Is there any way to save the trajectory with only water molecules within 5 A
of the protein to a DCD when "Update Selection Every Frame" is activated?



-----Original Message-----
From: [] On Behalf Of
Axel Kohlmeyer
Sent: Monday, November 15, 2010 5:23 PM
To: quantrum75
Subject: Re: vmd-l: Water molecules within a definite radius

On Mon, 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?

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.


> Thanks!
> Rama
> --- On Mon, 11/15/10, David Wedner <> wrote:
>> From: David Wedner <>
>> Subject: vmd-l: Measure Radius of gyration
>> To:
>> 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
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.