[gmx-users] minimum distance between periodic images does not aggree with box dimensions

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 1 14:59:56 CEST 2012

Hi Thomas,

The rhombic dodecahedron is built as a rectangular brick, which makes
it easy to fill with a rectangular bricklet of water. Now, for the
smaller distances the short edge of the rectangular brick is smaller
than the diameter of the particle, and it is represented fragmented.
Best way to get acquainted with this stuff is drawing a circle, and a
hexagon around it. Then tesselate a patch of space and draw the
corresponding rectangular cell. Try to translate the rectangle such
that the whole circle fits in. Good luck! :p

For the other thing, notice that the distance reported is close to a
bond length. Before checking the distances between periodic images,
make sure that the solute not fragmented...



On Mon, Apr 30, 2012 at 4:38 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> Dear GROMACS users,
> I have a nanoparticle (perfect sphere) and want to enclose it into a rhombic
> dodecahedron. For this purpose I use the following command lines
> editconf_d4.5.5 -f nano.gro -bt dodecahedron -d 1 -c -o nano_box.gro
> grompp_d4.5.5 -f em.mdp -c nano_box.gro -p nano.top -o nano_box_EM.tpr
> mdrun_d4.5.5 -v -deffnm nano_box_EM
> echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f nano_box_EM.trr -s
> nano_box_EM.tpr -o nano_em_dodecahedron.xtc
> echo 2 | g_mindist_d4.5.5 -f nano_em_dodecahedron.xtc -s nano_box_EM.tpr -pi
> -od nano_mindist.xvg
> The first paradox is that the nanoparticle is fragmented in the dodecahedron
> representation for -d (editconf option) less that 1 nm. The second paradox
> is that the minimum distance between periodic images for -d 0.5, 1, 2, 3 is
> 0.183, 0.237, 4.171 and 6.167 nm respectively. The last two distances are
> close to the expected values but the first two are far from them. I would
> expect ~1 and ~2 nm for -d 0.5 and 1 respectively, since by definition with
> option -d and dodecahedron, the dimensions are set to the diameter of the
> system (largest distance between atoms) plus twice the specified distance.
> Can anyone explain what's happening?
> Thanks in advance.
> Thomas
> --
> ======================================================================
> Thomas Evangelidis
> PhD student
> Biomedical Research Foundation, Academy of Athens
> 4 Soranou Ephessiou , 115 27 Athens, Greece
> email: tevang at bioacademy.gr
>           tevang3 at gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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