[gmx-users] increase membrane dimensions

edesantis edesantis at roma2.infn.it
Tue Apr 16 17:31:42 CEST 2019

Dear Gromacs users,

I want to simulate a protein embedded in a membrane made of POPC 

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 

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,

Dr. Emiliano De Santis, PhD

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