[gmx-users] regarding .gro file

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Nov 25 11:33:59 CET 2007


Maybe it's good to note that gromacs (mdrun) will always write the
coordinates such that the first atom of each molecule is located inside the
rectangular box spanned by the xx, yy and zz components of the triclinic
box, located at the origin.


On Nov 25, 2007 4:47 AM, Mark Abraham <mark.abraham at anu.edu.au> wrote:

> > Hi,
> >
> > Actually I started a simulation with bilayer. After energy
> > minimization I could see in ngmx the bilayer was at the middle of a
> > box and two layers of water are on both sides of it  and that was my
> > initial structure. After simulation of 1.5 ps the bilayer has moved to
> > one side of the box, with a thin layer of water in one side and
> > maximum number of water on another side of bilayer.  I want to
> > understand whether the whole bilayer is diffusing to one side of the
> > box or it is due to imaging problem. So I wanted to know the technical
> > way of writing .gro file by gromcas.
> The system's periodic, so there are an infinite number of equivalent
> representations. There is no "side" to the box. You can use trjconv to
> generate an acceptable look. See
> http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
> Mark
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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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