[gmx-users] What's the default pbc of Gromacs trajectories?

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 28 23:07:30 CEST 2008

LuLanyuan wrote:
> Hello,
> I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x.
> The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc.
> As I remember for early versions of Gromacs the default pbc of output trajectories was "whole",
> which means no broken molecules. But I just found it's not the case for the latest version, since
> I can see broken lipids for my membrane system using "ngmx". I'm just wondering what's the
> default pbc for the latest Gromacs version and whether there is a way to change it before MD
> simulations.

I think you are asking two separate questions.

 From trjconv -h you can find the default behavior for PBC treatment, which is 
"none," as in, leave the coordinates alone.

The PBC behavior of an MD simulation is specified in the .mdp file.  Removal of 
PBC from "broken" starting structures should be the first step in the simulation.


> Thanks for your help.
> Lanyuan Lu
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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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