[gmx-users] octahedron box shape problem

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 31 16:31:19 CET 2001

On Wed, 31 Oct 2001, thomas stockner wrote:

>applying a commands like:
>-editconf -f struc.g96 -o box.g96 -d 1.4 -bt octahedron -label A 
>-genbox -cp box.g96 -cs spc216.gro -o h2o.g96 -p struc.top 
>and creating a pdb file for visualizing with rasmol
>-pdb2gmx -f h2o.g96 -o rasmol.pdb
>the box I get is always recangular, independenty which options of editconf I 
>tryed (-bt; -angles; -box). 
>I don't understand, why the output of editconf regarding the box statistic 
>does not correspond to characteristics of the filled water box of the pdb 
>file visualised with rasmol.
>I cannot find the error I make. Could anyone help me to generate an 
>octahedron box.
You're not making an error. Gromacs represents the box the way it uses it
in mdrun. Use 
trjconv -ur compact -s topol.tpr -f file.pdb -o filenew.pdb

I will add an option to editconf to do the same thing (that way you won't
need a tpr file).

Having said all this, I can't make it work. Maybe Berk Hess cares to

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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