[gmx-users] Re: problems with editconf command

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 10 12:25:05 CET 2009

Please keep correspondence on the list.  If you want to post images, do so via 
the web so that everyone can have a look.

Andrew Voronkov wrote:
> Dear Justin,
> I am very sorry for writing to you directly, but seems like gmx user list doesn't like attachments. I have problems with editconf command line.
> I've used the command lines:
> editconf -c –f conf.gro –bt dodecahedron –d 0.5 –o box.gro - to get dodecahedron and to center the protein, then I've used:
> genbox –cp box.gro –cs spc216.gro –p topol.top –o solvated.gro
> But 
> 1) I get a cubic box, not dodecahedron

This is a VMD issue, not a Gromacs problem.  By default, VMD will display 
rectangular or triclinic boxes based on what it finds in the .gro file.

Use trjconv -pbc mol -ur compact to get a "correct" representation.

> 2) protein is not in the center of the box, but in the edge (see attachemnt screenshot).
> I've checked the flags -looks like they're ok, but seems like editconf doesn't see 
> -c flag and dodecahedron parameter.

Again, just a VMD thing.

> The initial conf.gro and topol.top are also attached.

These are not useful for diagnosis; the screenshot is enough.


> Best regards,
> Andrew
> ------------------------------------------------------------------------


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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