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
