[Fwd: Re: [gmx-users] problems with KALP-15 IN DPPC tutorial]

scaprari at uniroma3.it scaprari at uniroma3.it
Fri Feb 3 12:12:30 CET 2012

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,

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