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

Smith, Micholas D. smithmd at ornl.gov
Tue Nov 11 14:16:53 CET 2014

Two things to check: First try converting your trajectory to a pdb using trjconv instead of avogadro, as you can taken into account the perodic boundries. Second, ions can behave "oddly" in simulations due to hydration-effects; however, having them all cluster in a location is typically bad, as such  it is a good idea to check that the force-field and water model you are using are compatible with the concentration of ions you are using (typically you don't want to go above 0.5M if you can help it), a quick search in the literature should pull up some papers on this (I seem to have misplaced my copies at the moment).

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nima Soltani <nima.slt at gmail.com>
Sent: Monday, November 10, 2014 7:33 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

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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