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.scripps.edu på vegne av Mark Williamson
Sendt: ma 16.07.2007 16:52
Til: amber.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 18 2007 - 06:07:26 PDT
