Birgit Hischenhuber wrote:
Hi,
I simulate a molecule in a dodecahedron.
I used at the step with the editconf:
editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0
After my simulation I looked at the first frame and saw, that at two
direction the molecule is actually 2 nm away of my edge, but the at the
third edge the molecule is not in the middle, but near the edge.
I looked also at the other pdb-files with the water before the
simulation, and there the location of the molecule is the same, in my
opinion not in the middle of the body.
Is this a bug? Or have I done anything wrong?
There is no bug. The representation is simply a triclinic cell, and probably
periodicity effects. For visualization purposes only, you can "correct" the
representation with trjconv -pbc mol -ur compact.
-Justin
Thanks a lot for your helps!
Greets, Birgit
---
DI Birgit Hischenhuber
Unit for Medical Statistics and Informatics
Section for Biomedical Computersimulation and Bioinformatics
Medical University of Vienna
General Hospital
Spitalgasse 23, BT88
A-1090 Vienna
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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