Dear Gromacs users,
I want to simulate a protein embedded in a membrane made of POPC
phospholipid.
I have some experience with MD, but it is the first time that I am
simulating a membrane protein.
I am following the tutorial of KALP15 in DPPC membrane
(http://www.mdtutorials.com/gmx/membrane_protein/02_topology.html).
my problem is that I want to simulate a bigger protein respect to the
one in the tutorial and in order to avoid to have interactions among the
replicas, I need to have also a bigger membrane (more than 128 lipids,
that are in the equilibrated gro file)
how can I increase the dimensions of the membrane?
I could add (and subtract and the various combinations) to all the
phospholipid coordinates the sides of my simulation box, but my fear is
that in this way I would have collisions on the atoms at the box edges,
Is there a way of doing it using gromacs tools?
thank you in advance,
best
Emiliano
--
Dr. Emiliano De Santis, PhD
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