[gmx-users] Re: GMX 4.0 RC2: mdrun writes broken molecules?

[Bert]

 I have encountered the same problem too. For water molecules not being
broken in the mdrun, I think atoms in same charge group will not be divided
into separate processors. It will be ok to use trjconv -pbc nojump/mol to
get a clear visualization.

>
> Hi Justin,
>
> It's indeed the case that mdrun now writes broken molecules. Has to do
> with the domain decomposition and processors only keeping track of
> 'their' atoms. Too bad, but you'll just have to keep a .tpr around to
> make molecules whole again afterwards. Using trjconv -nojump with a
> suitable reference (not necessarily a .tpr) would also do it (and
> simultaneously remove the jumps...).
>
> Cheers,
>
> Tsjerk
>
> On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> > Hi,
> >
> > I've been running some simulations with Gromacs 4.0 RC2, and I've noticed
> > something strange.  In the output .gro file at the end of a run, the
> > molecules in my system (a membrane protein) are broken, crossing periodic
> > boundaries. This affects the lipids at the periphery of the box, in my
> case.
> >
> > Has there been some change since the previous version that mdrun is now
> > writing broken molecules to fit everything within the unit cell?  Or is
> this
> > behavior unintentional?
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > 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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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
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>
>
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