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. -- View this message in context: http://gromacs.5086.n6.nabble.com/Actual-box-size-tp5003850p5003858.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
