[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC
Eric Jakobsson
jake at ncsa.uiuc.edu
Sat Sep 10 13:36:26 CEST 2005
It is true that we did those studies in the Dark Ages (pre-PME). For a
straightforward test of pure VDW, we did constant pressure simulations of
hexane with different cutoffs, and found a plateau in the density above
15-20 angstroms, evaporation below 10-15 angstroms, varying density
between. In that case, we used each hexane molecule as a charge group. It
would be interesting to repeat that with each methyl and methylene group as
a charge group to see if a lower cutoff is o.k. in that case---unless you
have already done that simulation.
Eric
At 01:40 AM 9/10/2005, you wrote:
>On Fri, 2005-09-09 at 13:52 -0500, Eric Jakobsson wrote:
> > We never did a separate publication on this--it is just a couple of
> > sentences in one or our early papers--but one of the reasons we always use
> > 20 angstrom van der Waals cutoffs is that shorter cutoffs sometimes caused
> > bilayer separation. One thinks of the long range van der Waals as
> > unimportant because of falling off as the sixth power, but the other side
> > of the coin is that, unlike the electrostatic long range, all the long
> > range van der Waals is attractive; i.e., van der Waals forces are
> > essentially unshielded.
>
>The real problem is that in many topologies the charge groups are large,
>that means that the Van der Waals interaction can quite suddenly turn on
>on or off. If you use PME there is no reason for large charge groups and
>you can make them smaller, 2-3 atoms.
> >
> > At 12:24 PM 9/9/2005, David L. Bostick wrote:
> >
> > >Hello,
> > >
> > >If your bilayer separation is coupled to an unrealistic area per
> headgroup,
> > >you may have a poorly equilibrated system. If you can prescribe an
> area and
> > >run the bilayer for some time (1-2 ns) in a constant area, constant
> > >pressure ensemble, and then switch to semiisotropic pressure coupling,
> this
> > >could fix it. The same could be done with NVT, but again you will need to
> > >have a starting configuration with not only the correct area, but the
> > >correct density for water in the bathing solution.
> > >
> > >David
> > >
> > >
> > >
> > >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> =-=-=
> > >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, 9 Sep 2005, Louic Vermeer wrote:
> > >
> > > > Hi everybody!
> > > >
> > > > Thanks for your reply Andrey, unfortunately, it doesn't help a lot. I
> > > > already tried to use PME, but the bilayer separation remains (for POPC
> > > > only). g_rdf gives overlapping graphs for the water in all three
> > > > starting structures, so it is not dehydration that causes the
> separation
> > > > of the bilayer. I also tried pressure coupling:
> > > > >> When using pressure coupling the bilayer looks better, simply
> because
> > > > >> it is being "pushed back" by the applied pressure (1 bar). This,
> > > > >> however, does not remove the _cause_ for the lipids to move apart.
> > > >
> > > > Is there someone who has done NVT runs on POPC (or POPC/POPG)
> willing to
> > > > share his parameters? (Of course I looked in the literature, but this
> > > > did not get me all the info I'm looking for).
> > > >
> > > > with kind regards,
> > > > Louic
> > > >
> > > > Andrey V. Golovin wrote:
> > > > > Hi Louic!
> > > > > Yours case is quite strange.
> > > > > I used self assembled from random mixture DPPC and POPC bilayers and
> > > > > didn't notice any difference in behavior. I used Dr. Tieleman's
> > > parameters.
> > > > > But this situation that you mentioned I faced then I started
> dehydrate
> > > > > (remove water) from the system at the constant Z axis value.
> Water tried
> > > > > to form normal interaction thought PBC , and separating bilayer
> leaflets
> > > > > has been happened.
> > > > > So in your case I would check density of water in system and do some
> > > > > simulations with pressure coupling and PME electrostaics.
> > > > >
> > > > > Andrey.
> > > > >
> > > > > Louic Vermeer wrote:
> > > > >
> > > > >> Dear gromacs users,
> > > > >>
> > > > >> The issue of separating bilayer leaflets has been posted to this
> > > > >> userlist by others before me, but none of the solutions that were
> > > > >> sugeested seems to work for me. Therefore I decided to bother
> you with
> > > > >> a short overview of what has been posted before, as well as my
> > > > >> (detailed) question.
> > > > >>
> > > > >> When starting an md run on the POPC bilayer (popc128a.pdb) from Dr.
> > > > >> Tieleman's website[1], the bilayer leaflets move apart in several
> > > > >> picoseconds (not instantly), leaving a vacuum between them. This
> > > > >> compresses the water that is present. A funny thing is however, that
> > > > >> this does not happen to the DMPC and DPPC bilayers from the same
> > > > >> website, using the same parameters[2]. As far as I know, these
> lipids
> > > > >> do not differ that much[3]. I did not (yet) modify any of the files
> > > > >> mentioned.
> > > > >>
> > > > >> Previously, these suggestions have been posted to solve similar
> > > problems:
> > > > >> - use trjconv -pbc nojump
> > > > >> - try a cutoff distance of >= 2(nm)
> > > > >> - use pressure coupling
> > > > >> - use DispCorr = EnerPres
> > > > >> and recently something like:
> > > > >> - "be nicer to the lipids, maybe even use softcore."
> > > > >>
> > > > >> None of these options worked for me, though I must admit I do not
> > > > >> fully understand how to "be nice".
> > > > >>
> > > > >> When using pressure coupling the bilayer looks better, simply
> because
> > > > >> it is being "pushed back" by the applied pressure (1 bar). This,
> > > > >> however, does not remove the _cause_ for the lipids to move apart.
> > > > >> Also, NVT must be possible.
> > > > >> I could of course impose position restraints on the lipids, but this
> > > > >> doesn't sound like a good idea to me, because the reason for
> using MD
> > > > >> is studying dynamics, and not lipids that were nailed to a place
> where
> > > > >> they "look better".
> > > > >>
> > > > >> Anyone?
> > > > >> Help will -of course- be greatly appreciated. And since you made it
> > > > >> all the way to the end of my question: Thanks!
> > > > >> More detailed info below.
> > > > >>
> > > > >> Louic Vermeer
> > > > >> Biophysics group, Wageningen University, The Netherlands
> > > > >> IPBS, Toulouse, France
> > > > >>
> > > > >>
> > > > >>
> > > > >> details
> > > > >> ------------------------
> > > > >>
> > > > >> [1] http://moose.bio.ucalgary.ca/index.php?page=Downloads
> > > > >>
> > > > >> [2] .mdp-file, parameters that were used for the md run. When
> comments
> > > > >> (;) are used, different values of these parameter were tried in
> > > > >> different runs, but did not solve the problem described above.
> > > > >>
> > > > >> integrator = md
> > > > >> dt = 0.002
> > > > >> nsteps = 10000
> > > > >> comm-mode = Linear
> > > > >> coulombtype = Cut-off
> > > > >> rcoulomb_switch = 0
> > > > >> rcoulomb = 1.8 ;2.4 ;1.0
> > > > >> epsilon_r = 1.0
> > > > >> vdw-type = Cut-off
> > > > >> rvdw_switch = 0
> > > > >> rvdw = 1.4 ;2.2
> > > > >> DispCorr = EnerPres ;No
> > > > >> Tcoupl = Berendsen
> > > > >> tc_grps = POPC SOL
> > > > >> tau_t = 0.1 0.1 ;0,01 ;1
> > > > >> ref_t = 300 300 ;330
> > > > >> Pcoupl = no
> > > > >> annealing = no no
> > > > >> constraint_algorithm = Lincs
> > > > >> lincs-iter = 1 ;2 ;8
> > > > >> lincs-order = 4 ;8
> > > > >>
> > > > >> [3] Some differences between the lipids
> > > > >>
> > > > >> lipid chains MW
> > > > >> DPPC 16:0-16:0 734.05
> > > > >> DMPC 14:0-14:0 677.94
> > > > >> POPC 16:0-18:1 660.09
> > > > >> _______________________________________________
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> > > > >>
> > > > >
> > > > >
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> > ---------------------------------
> > Eric Jakobsson, Ph.D.
> > Professor, Department of Molecular and Integrative Physiology, and of
> > Biochemistry, and of the Center for Biophysics and Computational Biology
> > Senior Research Scientist, National Center for Supercomputing Applications
> > Professor, Beckman Institute for Advanced Science and Technology
> > 4021 Beckman Institute, mc251
> > University of Illinois, Urbana, IL 61801
> > ph. 217-244-2896 fax 217-244-2909
> >
> >
> >
> >
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>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
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