[gmx-users] Re: Actual box size

zugunder schlecht at mail.ru
Mon Dec 17 20:14:17 CET 2012

Thank you, Justin, for the prompt answer!

Justin Lemkul wrote
> In almost all cases, a dodecahedral box is the optimal choice.  A cubic
> box with the same periodic distance for an elongated protein would be much
> larger.

OK, got it. 

Justin Lemkul wrote
> In the absence of the actual editconf commands, it's hard to judge the
> utility of each of these setups.
> The box vectors shown are the ones that will be used unless you manipulate
> them in some way.

In this particular case the commands were:

g_editconf -f protein.gro -o protein_box.gro -bt triclinic -d 1.0 -c
g_editconf -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.0 -c

and my concern is that the reported box volume in case of dodecahedron is
much bigger than that for a triclinic one (for the same protein). Sure, the
triclinic box volume is calculated from vectors 100% correctly, and I guess
that it is correct for dodecahedron as well 

> And I have one more short question:
> Is it possible somehow to visualize the "actual" dodecahedral box at this
> stage (i.e. right after adding water, having no trajectory file yet)?

Justin Lemkul wrote
> You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
> mol -ur compact.

So I need to run at least genion first. Got it.

Thank you.

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