[gmx-users] Re: Actual box size

[zugunder]

Justin Lemkul wrote
> It is calculated correctly, the math is just a bit more complex (see the
> manual for the equations).  The distance to the box edge is defined the
> same way, but the two approaches don't necessarily give equally suitable
> results.  Consider the first case, which produces a rectangular box from
> an elongated configuration.  If your protein rotates 90 degrees about the
> z-axis, you will likely violate the minimum image convention, as the box
> vector along y is insufficient to accommodate the protein.  Problem!  The
> dodecahedral box is pseudo-spherical and thus, regardless of how the
> protein rotates, the minimum image convention is not violated.

So, in other words, the safest way for an elongated protein (with no
restrictions on rotation) is either a cube or dodecahedron, because only in
these 2 cases only the longest dimension of the protein is effectively taken
into account - do I understand it correctly? And obviously, this is true for
any almost-spherical protein as well...

And, therefore, any rectangular box, different from a cube will bring to a
violation of the minimum image convention in case of unrestricted rotation
of an elongated protein around its shorter axes assuming we set the same -d
as in case of a cube? So do I get it right that non-cubic rectangular boxes
are used only in such specific cases with restrictions on rotation?

Thank you.



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