[gmx-users] Creating water slabs on bilayer headgroups

David L. Bostick dbostick at physics.unc.edu
Tue Aug 9 19:07:54 CEST 2005

Hello Farid,

Make the water box 8 7 2 for each monolayer or 8 7 4 for the whole slab,
and shift it above/below the bilayer using editconf.
See below ..  I have done this several times when creating bilayers, and it

You need to shift the z-dimension of the water slab up such that it has
roughly a 2 Angstrom clearance over the headgroup atoms.  You can do the
same for the slab of water on the lower side of the membrane.  Depending on
the type of lipid, it is very important you have a good amount of hydration
water.  If you want to be relatively safe, here's what I'd do.  Create a
single slab
of water ~50-60 Angstroms thick (5-6 nm), and shift the whole thing above
your bilayer with ~2 Angstrom clearance using editconf.  Periodic boundary
conditions will take care of the rest. You can probably get by with less
water, .. it's your system, and you can make the judicious choice. If you
want the bilayer placed neatly in the center of the box, do editconf with an
index file for your system with the -c option, and choose the lipid molecules
for the group to center. You will then get half the water slab hanging outside
the box.  The water will be wrapped around before doing your first calculation with
mdrun.  If you want to "wrap" the water before running just to look at it,
use trjconv with the -pbc whole option.

I would also sugest that before you begin running seriously, you do a
pre-equilibration with Berendsen semiisotropic pressure coupling with

compressibility         = 0.0 4.5e-5

to hold the x/y directions stiff, keeping the area per headgroup the
expected value until the water reaches equilibrium, and the lipid tails
become a bit disordered. Once all is well, you can switch to

compressibility         = 4.5e-5 4.5e-5

for a real equilibration.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Tue, 9 Aug 2005 fsaadedi at staffmail.ed.ac.uk wrote:

> Dear David,
> Unfortunately the spc molecules are still located throughout the bilayer.  Are
> there any commands available to have them just localised to the headgroups?
> Farid
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