NAMD Question: Generating ensemble of structures

From: Oscar Bastidas (
Date: Wed Aug 31 2016 - 00:52:20 CDT


I am a novice at using NAMD and I have a question on whether the NAMD
software can be implemented to provide as output PDB structures at regular
intervals (specified by me in accordance with my total running simulation
time) such that I end up with an ensemble of structures similar to the
ensembles provided by protein NMR structure elucidation studies. I am
interested in knowing, if this is possible with NAMD, how it would be
implemented. Would you please tell me if to your knowledge this is a
possibility with NAMD and how I would go about to do it?

If this is not a possibility, then I am open to the following alternative,
again, if it is possible: Can I have NAMD produce a final PDB structure at
the end of a simulation for a certain amount of time and, then, once that
simulation is finished, feed this output PDB structure that shows the final
trajectory stopping point as the input PDB into another separate simulation
run? As you might imagine, I'd intend on repeating this multiple times
(I'm specifically interested in obtaining an ensemble of 10 structures) to
obtain superimposable structures that would ultimately resemble the
aforementioned NMR ensemble, but show the actual range of true motion of
the protein (like strobe photography of a golfer). Thank you for any help
you can provide.

Respectfully submitted,

Oscar B.

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