AMBER Archive (2007)

Subject: SV: AMBER: Atoms in contact to a specific atoms during MD

From: Rafi Ahmad (Rafi.Ahmad_at_fagmed.uit.no)
Date: Mon Jul 16 2007 - 10:04:46 CDT

Thanks for the reply.
 
This is just for one trajectory and can be easily done with many other tools.
 
But what I would like is to get it for all snapshots (i have 10000 of them). Meaning during all those snapshots what atoms are close to say atom "X".
 
Rafi

________________________________

Fra: owner-amber_at_scripps.edu på vegne av Mark Williamson
Sendt: ma 16.07.2007 16:52
Til: amber_at_scripps.edu
Emne: Re: AMBER: Atoms in contact to a specific atoms during MD

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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