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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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