[gmx-users] PBC

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 16 15:14:31 CEST 2009

Andy Torres wrote:
> Hi, I would like to know if there a way to do an isolated protein 
> simulation (without periodic boundary conditions) and in that case, how 
> can I choose the bondary conditions.
> I`ve been reading editconf  opcion -pbc, and pbc  =  no in the .mdp 
> files, but it doesn`t seems to work.

Well, edticonf -pbc has no relevance; it is used to reconstruct molecules split 
over periodic boundaries.  Using pbc = no in the .mdp file is what you want.  If 
something is going wrong, you'll have to describe your problem more thoroughly, 
instead of simply claiming it doesn't work.


> Hopping to be clear,
> Thanks in advance!
> Andy
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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


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


More information about the gromacs.org_gmx-users mailing list