[gmx-users] Re: grompp for minimization: note & warning

Justin Lemkul jalemkul at vt.edu
Mon Sep 16 16:58:01 CEST 2013

On 9/16/13 10:52 AM, shahab shariati wrote:
> Dear Justin
> Very very thanks for your quick reply.
>> The sys.gro file is positioned within a box that is too large, a fact that is
>> easily observable in VMD.  I suspect that the void space results in instability.
> If I positioned system in a smaller box, my problem  (instability) solved ???

I have no idea.  I don't know how the box was set or why it was set in that way. 
  It's certainly wrong, but it may not solve the underlying issue.  Visualize 
the area around the drug - there is severe atomic overlap between the lipids and 
the drug molecule.  Clearly it was not built in a manner that will be stable.

>> As for the charge group error from grompp, I still can see no reason for it.
> In the first e-mail, I put charge groups, as you seen, they were ok and true.
> Thus what is reason of charge group error from grompp.

As I said, I don't know.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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