[gmx-users] Regarding membrane(DMPC) simulations with fullerene
jalemkul at vt.edu
Wed Oct 23 00:16:50 CEST 2013
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:
Justin A. Lemkul, Ph.D.
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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