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

Justin Lemkul jalemkul at vt.edu
Tue Nov 11 01:39:45 CET 2014

On 11/10/14 7:33 PM, Nima Soltani wrote:
> 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):
> https://www.dropbox.com/s/smabls57wj4pvtm/md_0_1.pdb?dl=0
> 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?

You also have a line of waters doing the exact same thing.  The conversion of 
.gro to .pdb has totally botched the coordinates.  If you want .pdb format, just 
use editconf, rather than some external program which is clearly misformatting 
or misinterpreting the contents of the file.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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