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

Justin Lemkul jalemkul at vt.edu
Mon Sep 16 16:13:27 CEST 2013

On 9/16/13 9:47 AM, shahab shariati wrote:
> Dear Justin
> My input coordinate file is a gro file (sys.gro). When I visualize that by VMD,
> all things is ok and true.
> After minimization, I obtained a gro file (em.gro). When I visualize that by
> VMD, About 5 DOPC molecules leave bilayer structure and 1 DOPC molecule not only
> leaves bilayer structure, but also some bonds were broken (there is a broken
> molecule). Before, I mentioned that my input coordinate file (em.gro) is
> obtained from reliable website. How to resolve this issue?
> I attached 2 gro file (sys.gro and em.gro). Resolvation of this issue is very
> critical and important for me. Please guide me about that.
> Excuse me for sending this e-mail to personal address. I have to send 2 gro
> files to you.

The proper protocol is to upload the files somewhere publicly accessible and 
post a download link.  I generally do not like large, unrequested attachments.

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. 
  As for the charge group error from grompp, I still can see no reason for it.



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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