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

Thomas Evangelidis tevang3 at gmail.com
Mon Apr 30 16:38:16 CEST 2012

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 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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