[gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

Nima Soltani nima.slt at gmail.com
Tue Nov 11 01:33:27 CET 2014

Hi everyone
I am following excellent Gromacs tutorial that is provided by Dr. Justin
Lemkul, First of all i want to thank him for taking time to provide such an
excellent tutorial.
My Question is about final structure of protein and ions after runing final
Molecular Dynamic simulation of the last step
Here is link of my final structure that i get after simulation -after
converting it from .gro file to .pdb file (by Avogadro program):
i find out that all CL ions are in a strange position far away from protein
at edge of the box, well i suppose that negative Chlorine ions should be
away from each other (same charge) and close to protein which has positive
charge. which is not!
is my simulation is incorrect?
if not what cause this seemingly strange thing to happen?
Thanks in advance for any guidance

Best Regards,
Nima Soltani
Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.

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