I accomplished the steps related to the removal of the periodicity by my patch of membrane and to the extension in order to build a bigger bilayer. The resultant structure appears good.. Now, I'm wondering how to define my box which will be used to perform the solvatation step. I am new in GROMACS (version 4.0.7) and I need to carry on the dynamics simulation of the phospholipase protein when this latter leans on the surface of the membrane (so the protein is not embedded into the membrane but just leant on that). So far, as I mentioned above, i made the extension of my dppc128 patch of membrane (I have used nbox parameters 4 4 1).At this point, Have you got any idea about the parameters necessary to build the box and to do the solvatation? Shall I to consider even my protein during these steps?How? Any suggestion will be appreciated, Silvia
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