[gmx-users] What's the default pbc of Gromacs trajectories?
lulanyuan at msn.com
Tue Jul 29 01:12:32 CEST 2008
Thanks for your reply. I just checked the online manual for .mdp. But I didn't find
an option to change output pbc types. If I need the output trr file to be "whole" as
that from an older version, can I set it up anywhere?
I understand I can use trjconv to convert trr files. But usually trr files are huge and
the convertion takes time.
> Date: Mon, 28 Jul 2008 17:07:30 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories?
> 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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