From: Richard Law (
Date: Mon Feb 05 2007 - 12:49:07 CST

Yes - the vmd membrane plugin uses pre-prepared membrane patches
(pope_box.pdb, etc.) that are somewhat ideal (doesn't really matter if you
equilibrate them right) but they suffer from the tails being very slightly
interlaced. Due to the lipid density being initially too low, as you
equilibrate they can overlap the tails which has two problems: a) the lipid
per area will never get much closer to being right, and b) the center of the
bilayer enters a sort of gel phase (I'm quoting someone else here that I was
talking to about this last week - he can identify himself if he wants to!).

So you need to equilibrate initially holding the headgroup z-coords to let
the tails melt and allow the density to increase, for at least 500ps -
probably more like 1-10ns. (Maybe in reality equil would really take
10-100ns but the area per lipid may never be equal to experimental values
(there are papers on this already)) This would be under NPT.

Once you've got it set, let the headgroups go and use constant area to keep
your lipids at the area per lipid you got - although you'll have to go
through the whole process again once you insert a protein into your
equilibrated bilayer! (This is harder than it sounds but there was a
discussion on one of the many ways to do this, recently.)

I don't think these "plug-and-play" membrane patches were intended to be
realistic without some work. They're just good because they're easy to use
and easy to minimize.

And so ends the membrane plugin 101 class. There will be a multiple choice
quiz at the end of the week.


p.s. there are other membrane patches out there and writing a simple script
to patch them together yourself, or even calling it popc_box.pdb and
sticking it in the membrane plugin directory would probably help you out a

On 2/5/07, Himanshu Khandelia <> wrote:
> If one generates a POPE membrane using the vmd plugin, the resulting area
> per lipid is about 71 A^2 per lipid [example, a 100 x 100 patch has 140
> lipids in each leaflet]. This area per lipid is about 17% higher than the
> experimentally measured values at 30-40 degree C. However, the average
> bilayer thickness (phosphate-to-phosphate) is about 38 A, which is more or
> less as expected in experiments.
> It this initial membrane setup not too far from equilibrium ? Of course,
> one could equilibrate to the correct area per lipid, but that would
> require holding the headgroups constrained along the bilayer normal, so
> that the bilayer thickness does not increase while the area gets reduced.
> However, I have not really come across this method/discusssion/problem in
> any articles where VMD's plugins have been used. What am I missing ?
> -Himanshu
> P.S: I think this post is relevant to both vmd and namd forums, and have
> copied it to both.

Dr. Richard J. Law
Biosciences & Biotechnology Division
Chemistry, Materials and Life Sciences Directorate
Lawrence Livermore National Laboratory
L-372, 7000, East Ave,
CA.  94550  USA
tel: +1 925 424 2338
fax: +1 925 422 4665