VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun May 21 2017 - 18:00:34 CDT

Yes, it should be simple enough but to answer your question one would need
to know:
What is your definition of "Not in contact"? Are there some lipids
covalently linked to the polymer? and others are not? Or do you mean you
want to pick out those lipids which are not within a distance cutoff of
your polymer?

Have a look at these for usage of atomselect :

http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node109.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node181.html

For more complicated selections have a look here:

http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node142.html#SECTION001082000000000000000

You have to create your own command - yes if you can think of it, it can be
done. The command will depend specifically on how your system is setup. If
the above links don't help, write back with more details about your system
and someone should be able to help you out.

Best,
/A

On Sun, May 21, 2017 at 11:39 AM, Mihaela Drenscko <quo.physics_at_gmail.com>
wrote:

> Dear users,
>
> I have a polymer in a lipid bilayer and I need to select for analysis only
> those lipids not in contact with the polymer. Does anyone know if there
> is such a selection procedure that can be done in VMD?
>
> Thank you,
> Mihaela
> 

-- 
Best,
/A