On 10/22/13 9:15 AM, Sathish Kumar wrote:
Dear Sir,
I am doing fullerene interaction with DMPC , i downloaded
the gro file from the website mentioned in the tutorial. I was keep the
fullerene on the top of DMPC. But in the gro file already water is present.
If i removed that water molecules and adding new water molecules by using
genbox command and afetr the running energy minimization the lipid
structure was collapsed. it is not like initial structure and some gaps
were found in the middle of membrane.
By keeping the water molecules as such
from the gro file and i keep the fullerene above the membrane then the
presented water molecules were randomly distributed inside the membrane,
and structure of water was distrubed.
If i added water using genbox to the membrane( with water from gro file),
there is a seperation found between two water layers.
All of the above outcomes simply suggest that you're not building the system in
a sensible manner. Without exact commands and some images of what you're
getting, there's nothing that anyone can really do to help.
Energy minimization was not running in all above cases.
How can i run this simulation please suggest me
Is there any tutorial like this simulation.
If it's not linked on the Gromacs website and Google can't find it, then no.
Tutorials don't exist for every iteration of a task. You want to place a
molecule at some location relative to a membrane; that's not significantly
different from the simple concepts described here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html
-Justin
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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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