VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 05 2007 - 14:52:48 CST

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:
  http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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 <hkhandel_at_memphys.sdu.dk> 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
> http://www.llnl.gov/bio/people/law/index.html
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 

-- 
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