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

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 3 14:36:17 CET 2012

scaprari at uniroma3.it wrote:
> 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?

Leave the x and y dimensions alone and adjust z only using editconf to 
accommodate whatever elements you're adding to the system.  You'll need 
sufficient room for your protein plus extra to avoid spurious PBC interactions 
(i.e. minimum image convention).  Positions of any molecules can be set using 
editconf, and general information about how to manipulate such things can be 
found in the following tutorial:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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