[gmx-users] Last step before CG em.mdp

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 1 19:11:57 CET 2009

Francesco Pietra wrote:
> Is anything recent to account for (and eliminate) clashes - if any -
> resulting from solvating a system of protein partly immersed into a
> canonical DPPC bilayer? That is, the solvation water  faces three
> different environments: the extracellular portion of the protein, the
> two water layers of DPPC, and the DPPC molecules themselves.
> I was comfortable to this regard (in all-atoms) with Chimera followed
> by Amber minimization. I have to re-educate myself with
> gromacs-martini. With cg Chimera has so many limitations.
> I assume (for cg) that the box should first be defined with editconf
> and then solvation (-cs water.gro) carried out with genbox.

In principle, with a suitably-defined box, there should be no issue.  I have 
seen numerous reports of MARTINI CG membrane proteins simulated with Gromacs in 
the literature, so it certainly works :)



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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