Re: vmd-l: Re: too large an area/lipid in POPE bilayers using membrane plugin

From: Richard Law (
Date: Mon Feb 05 2007 - 15:08:05 CST

Well yes but even that is a bit vague when it comes to some of the finer
points of membrane equilibration. It could definately be updated to make
it more fool proof. Maybe I should do that!

There's more than one way to skin a cat, with this issue, though. (I
apologise to any confused foreigners for how badly that metaphor probably


On Mon, 5 Feb 2007, John Stone wrote:

> Hi,
> I should point out that Richard has previously written a short
> tutorial that may interest people that want to go farther
> than what the membrane plugin will do for them:
> Cheers,
> John Stone
> On Mon, Feb 05, 2007 at 10:49:07AM -0800, Richard Law wrote:
>> 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.
>> Rich.
>> 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
>> little.
>> 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.
>> --
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++YNWA
>> Dr. Richard J. Law
>> Biosciences & Biotechnology Division
>> Chemistry, Materials and Life Sciences Directorate
>> Lawrence Livermore National Laboratory
>> L-372, 7000, East Ave,
>> Livermore.
>> CA. 94550 USA
>> tel: +1 925 424 2338
>> fax: +1 925 422 4665
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: Phone: 217-244-3349
> WWW: Fax: 217-244-6078

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