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

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Oct 5 20:50:47 CEST 2008

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...).



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
P: +31-30-2539931
F: +31-30-2537623

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