On Tue, Dec 30, 2014, Parker de Waal wrote:
>
> Currently I’m simulating a protein-protein complex membrane system
> and need help to re-image the protein complex to avoid complex-complex
> interaction through the periodic system.
Imaging never changes any interactions in the system, or its energy. It
simply collects molecules into a single unit cell, which is useful for
visualization or for certain types of geometric analyses (i.e. calculations
that don't know about periodic symmetry).
If you have an unwanted close contact with a periodic image, you are pretty
much stuck with it. Post-processing won't get rid of it, and if the clash is
severe, you may need to run a simulation with a bigger periodic box.
(Apologies if I have misunderstood your question.)
....dac
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Received on Mon Dec 29 2014 - 19:00:03 PST
