[gmx-users] Visualizing non-rectangular boxes

Ignacio Fernández Galván jellby at yahoo.com
Tue Oct 16 10:54:45 CEST 2007

--- chris.neale at utoronto.ca wrote:

> Yes. I use 3.3.1. Try installing that. If it works fine with 3.3.1
> and not with 3.3.2 then submit a bugzilla.

OK, I think I found it. Indeed, it works with 3.3.1 but not with 3.3.2.
After checking the source code, it works with 3.3.2 if I use this
command line:

trjconv -f b.gro -s b.tpr -pbc atom -ur compact -o c.gro

(note: -pbc atom)

There is a small confusion, because the help text for trjconv says:

Option -ur sets the unit cell representation for options mol, res and
inbox of -pbc.

But the "inbox" option is not allowed for -pbc. Instead it should say
"atom" (which translates to "bInBox" in the source).

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