[gmx-users] Visualizing non-rectangular boxes

[David van der Spoel]

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).
> 
> 
>       ___________________________________________________________ 
> Want ideas for reducing your carbon footprint? Visit Yahoo! For Good  http://uk.promotions.yahoo.com/forgood/environment.html
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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