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

Sathish Kumar sathishk238 at gmail.com
Tue Oct 22 15:15:32 CEST 2013

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.

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.

Thank You.


More information about the gromacs.org_gmx-users mailing list