[gmx-users] problems with PBC in editconf

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 14 17:18:51 CEST 2008

Rebeca García Fandiño wrote:
> Hello,
> I would like to transform to pdb a .gro file I have obtained from an 
> equilibration in Gromacs. I have tried directly with editconf:
> editconf -f equilibrated.gro -o equilibrated.pdb
> but the lipids of my membrane appear divided due to PBC.
> Then I have tried:
>  editconf -f equilibrated.gro -o equilibrated.pdb -pbc
> and they don´t divide, but the membrane and protein are in a side and 
> the water and ions in the other side. They are not where they should be.
> How could I convert a .gro file to a .pdb with no PBC and in the right 
> place, like the output file of a NAMD or AMBER program?

If you're correcting for PBC, the best tool is trjconv.  Explore the -pbc and 
-center options to compensate for periodicity.


> Thank you very much for your help in advance,
> Rebeca García Fandiño
> Parc Cientific of Barcelona
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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