[gmx-users] Visualizing non-rectangular boxes

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 16 11:57:17 CEST 2007

Ignacio Fernández Galván wrote:
> --- 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)
you can also use -pbc mol

> 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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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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