[gmx-users] problems with PBC in editconf

Rebeca García Fandiño regafan at hotmail.com
Thu Aug 14 17:13:53 CEST 2008

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?
Thank you very much for your help in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
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