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

[Thomas Evangelidis]

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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