[gmx-users] Regarding membrane(DMPC) simulations with fullerene

Justin Lemkul 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.
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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