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: [EMAIL PROTECTED]
> To: [email protected]
> 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
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Department of Biochemistry
Virginia Tech
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