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

[Justin Lemkul]

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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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