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

From: Mark Williamson <Mark.Williamson.imperial.ac.uk>
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:

        Graphics->Representations

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.

regards,

Mark Williamson
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Received on Wed Jul 18 2007 - 06:07:26 PDT
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