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

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 30 17:51:13 CET 2009

Francesco Pietra wrote:
> Hi:
> This is to ask how to proceed to minimize a CG ensemble made of a
> transmembrane multimer with pore region immersed in a hydrated DPPC
> bilayer and extracellular region immersed in water. Total height 18
> nm, width 10 nm in the extracellular region and 6 nm in the pore

Are these the dimensions of your protein?

> region. No clashes/contacts at 1 Angstrom vdw overlap. That is,
> cavities had been created - in two steps - with 2.5 Angstrom margin
> into both the bilayer surrounding the pore  and the water surrounding
> the extracellular region.
> Everything worked fine up to creating the topol.tpr, perhaps using a
> too small -box 15 15 15. Minimization by steepest descents (em.mdp
> below)

That box is clearly too small to accommodate your system, given the dimensions 
listed above.

> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC

You're using SPC water in a coarse grain model?  This doesn't make sense to me - 
an atomistic solvent with CG protein?


> The commands:
> genbox -cp my.pdb -box 15 15 15 -o my.gro

Indeed, this would call spc216.gro as the default solvent (-cs), which I don't 

> and then the system topology with
> grompp -f em.mdp -c my.gro -p my.top -o topol.tpr
> and then
> mdrun -v -s topol.tpr
> ==============
> I found no way to build the system using gromacs scripts alone, i.e.,
> combining preformed gromacs canonical boxes. The way I described above
> works fine in Amber with all-atom ensemble.
> ==========

It's been many weeks now that you've posted some issues with your CG system, and 
I'm sorry but I can't recall - have you run through my membrane protein 
tutorial?  It should be easily quite extended to a CG system.  All of the 
fundamentals are the same as far as positioning the system, etc. go:


> I would appreciate very much an opinion about the feasibility of such
> an approach with gromacs, or, hopefully, if a further solvation step
> is needed before minimizing. I did not try with a larger box, or if
> the protein+DPPC alone should be solvated with gromacs commands (I
> avoided this way because I want to leave the DPPC not solvated from
> the sides)...

Such systems can certainly be built with Gromacs.  Unwanted solvation comes from 
improper box definition.  I believe I suggested this before - don't define the 
box when using genbox, which uses a tiled algorithm to fill the unit cell.  Do 
all box manipulation and positioning with editconf.  I have found it to be more 



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


More information about the gromacs.org_gmx-users mailing list