[gmx-users] lipid bilayers jumping out of the box

David L. Bostick dbostick at physics.unc.edu
Fri Jul 8 20:28:40 CEST 2005


There is nothing wrong with your initial pdb file per se. It's just that
gmx likes to do periodic boundary conditions (pbcs) such that the center of
the system is around Lx/2, Ly/2, Lz/2. That is, for a cubic box of say
length L, the box will be taken to reach from 0 to L in all 3 dimensions.
The way you set up your initial system ( with the center at the origin), the
box would reach from -L/2 to L/2 in each dimension. To fix this, try

editconf -f orig.pdb -o out.pdb -c

where orig.pdb is your initial configuration centered at the origin. Then
use out.pdb with mdrun.

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 Fri, 8 Jul 2005, mark vaughn wrote:

> I have been experimenting with making bilayers of complex composition.
> I put together a low-density bilayer from the pdb files of several
> lipids translated to desired points, then rotated to not overlap with
> its neighbors--sort of a home written genconf with the capability of
> using an arbitrary number of pdb structures stacked at arbitrary
> locations. The longest acyl tails of each leaflet are aligned on a given
> z-plane,  then translated so that the initial separation between
> leaflets of 0.2 nm.  I generally center this homemade bilayer on the
> origin. I put it in a vacuum box using editconf with the -d option . VMD
> shows a nice organized bilayer. I expand the z-coord of the box, do an
> energy minimization,then compress it, either with position restrained md
> to a reference configuration or by scaling it to a higher density.
> However there is an annoying problem: every time I use mdrun (em, pr,
> whatever) the structure immediately jumps out of the box, so I end up
> with half bilayers with vacuum in between or other weird configurations.
> When i put water in later on, same problem.  Okay, the bilayers can all
> be put back together with trajconv, but it is troublsome to do so.  My
> main question, though, is what is wrong with my original pdb that makes
> the bilayers jump out of the box?
> thanks
> mv
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