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

[Justin A. Lemkul]

LuLanyuan wrote:
> 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?

What you are probably seeing is a visualization artifact, but you haven't 
described things very thoroughly.  In fact, mdrun does not write broken 
molecules; everything should be whole.  Like I said before, as soon as you start 
a simulation, all "broken" molecules are made whole.  Such behavior is defined 
in the topology.  If there is a bond between two atoms at a given distance, 
mdrun knows these atoms are bonded, even if they initially appear across the box 
from each other.

> I understand I can use trjconv to convert trr files. But usually trr 
> files are huge and
> the convertion takes time.

So write your output in .xtc format.  Use the nstxtcout option in the .mdp file.

-Justin

> Thanks,
> Lanyuan Lu
> 
>  > 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.
>  >
>  > -Justin
>  >
>  > > 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
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================