On Tue, Jul 11, 2017, Dan Roe wrote:
> Wow - this is certainly a challenging system to image! No one molecule
> can be considered "center" - in fact, there isn't even a region of a
> molecule that can be considered to be the center since when the
> hexamer is formed there is a large empty space in the center (from
> looking at the system this appears to be the way it should be
> assembled).
I can't offer much help now, but will take this opportunity to offer
some cautionary advice for future simulations:
1. Always use ioutfm=1 (the default, except in rather old versions of Amber)
2. Avoid using iwrap=1 for anything involving much more than
a monomer (or perhaps dimer) and mobile water and ions.
[If you are worried about precision loss because of not wrapping on the fly,
center and autoimage a restart file occasionally. Check visually that
the imaging "worked", then used the revised restart file to continue the
simulation.]
3. Use a big enough box. For a large box, it's easier to figure out how
to pack everything together into a single unit cell than for a smaller one.
...dac
p.s.: I actually think point 2 above should be "don't use iwrap=1, period."
But I'm open to counterarguments.
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Received on Tue Jul 11 2017 - 10:30:03 PDT
