VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 18 2010 - 04:01:00 CDT
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On Wed, Aug 18, 2010 at 2:14 AM, deepti nayar <deeptinayar_at_gmail.com> wrote:
>
>
> Hi all
>
> I want to find out the residues that are interacting with water in a
> trajectory. Is there any script for this in vmd?
you don't need a script for that. _all_ residues are. always!
i suspect, however, that the question that you want to ask
is not actually the one from above. you probably wanted to
ask which residues interact less strongly than a specific
energy cutoff value with water. remember how long-ranging
coulomb interactions are!
if that is the case, the answer is no and yes. VMD itself
is a viewer and as such has _no_ idea of the physics
of the model that you are simulating and thus cannot
give you an answer to that kind of question. it can, however,
generate inputs for a custom simulation (or single point
energy evaluation) e.g. via the namdenergy plugin and
return that result.
i suggest you rethink your question and then look up
the plugin and namd documentation to see how to proceed.
cheers,
axel.
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> -
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-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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