VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Mar 18 2018 - 07:50:26 CDT

Do you mean you want to measure/monitor the distance between "a molecule A"
and a "water molecule" in your simulation? The word trajectory update is
confusing.

If you just want a distance between two molecules listed for every frame of
your trajectory -- then you should know that a distance can only be
calculated between two points. Molecules have more than 1 point point so
you will have two decide which point to use as reference. You can choose an
atom or select a centre of geometry/mass and measure distance between that
for two molecules.

To measure distance look at the command measure bond (
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html)

For this I don't think you can use anything else apart from atoms, meaning
this won't work with centre of mass/geometry.
Try this. Drop back if it doesn't work and someone can help more. This is
obviously assuming I understood your problem correctly.

On Sun, Mar 18, 2018 at 7:31 PM, Udaya Dahal <dahal.udaya_at_gmail.com> wrote:

> Hi,
>
> I would like to extract the data as in visualization without trajectory
> update. For eg. I am looking at water molecules at some distance from
> another molecule A. If I don't update the trajectory, I can see the water
> moving away from the initial distance. How to extract this data in text
> mode? I appreciate your help.
>
> Regards,
> UD
> 

-- 
Best,
/A