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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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