VMD-L Mailing List

From: michaelmorgan937_at_gmail.com
Date: Thu Aug 25 2022 - 17:15:07 CDT

Thanks. Can I do it in VMD (adding an additional atom to trajectory)? The trajectory file was generated by CHARMM.

From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Wednesday, August 24, 2022 5:17 PM
To: michaelmorgan937_at_gmail.com
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: rdf with respect to a specific point

 

The way to do this is to add this position as an additional atom to your trajectory. 

--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!7MqqskhhQnGOu8xlZJOJJDcMdZvpFJ9Kinw8b65pvQ21puziuM8rpAnvafasbvFb-w5LgitdREkZPwSWx5urgWxd0YP7$  
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy
 
On Wed, Aug 24, 2022, 15:02 <michaelmorgan937_at_gmail.com <mailto:michaelmorgan937_at_gmail.com> > wrote:
Dear all,
 
I have a DCD file and I would like to perform rdf analysis around a specific xyz point (which is not occupied by any atom). Can I use the g(r) plugin for the purpose? It seems in the 
plugin I need specify two selections but how to specify this empty position? If cannot do it with g(r), what’s other choice in VMD?
 
Thank you very much.
 
Michael M.