Re: AMBER: Atoms in contact to a specific atoms during MD

From: Mark Williamson <>
Date: Mon, 16 Jul 2007 15:52:39 +0100

Rafi Ahmad wrote:
> I am trying to find out about all other atoms that are in certain radius
> to a specific atom during the complete MD simulations.

One solution is to use VMD. Having opened the trajectory, navigate
VMD's, menus as follows:


Then in the "selected atoms" box, type:

        all within 5 of name C1

and hit return,to show all atoms within 5A of atom name "C1". C1 is an
example here, it will be difference for you case.


Mark Williamson
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 18 2007 - 06:07:26 PDT
Custom Search