AMBER Archive (2007)

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

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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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• Next message: Rafi Ahmad: "SV: AMBER: Atoms in contact to a specific atoms during MD"
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• In reply to: Rafi Ahmad: "AMBER: Atoms in conatct to a specific atoms during MD"
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