[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC
David
spoel at xray.bmc.uu.se
Sat Sep 10 22:32:24 CEST 2005
On Sat, 2005-09-10 at 15:07 -0500, Eric Jakobsson wrote:
> Has anybody implemented and reported on how to do an inhomogenous
> dispersion correction? We thought about that but could not arrive at an
> algorithm that seemed worth investing a lot of human and computer time in
> trying.
For a membrane using PBC one could conceive a dispersion correction the
varies with the Z-axis (perpendicular to the membrane). That is, in the
Z-direction it would be constant, but the value parallel to the membrane
would vary along the Z-axis. On the other hand it is only important for
the pressure and since that is a global variable it doesn't matter.
For non periodic systems it has been used, e.g. Wensink et al. Langmuir
16 (2000) p. 7392, there a constant force in one direction was applied
to all particles.
>
> At 09:12 AM 9/10/2005, you wrote:
> >On Sat, 2005-09-10 at 06:36 -0500, Eric Jakobsson wrote:
> > > 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.
> >It would be good to do it, for inhomogeneous systems like membrane/water
> >interfaces you might want to try with an inhomogeneous dispersion
> >correction as well (different perpendicular and parallel to the
> >membrane). Or maybe that isn't necessary...
> >
> >By the way in the 3.3 code Berk has implemented dispersion correction
> >for shifted potentials as well.
> >
> > >
> > > 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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> > > > > >_______________________________________________
> > > > > >gmx-users mailing list
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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
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > gmx-users mailing list
> > > > > gmx-users at gromacs.org
> > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > >--
> > > >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
> > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > >
> > > >_______________________________________________
> > > >gmx-users mailing list
> > > >gmx-users at gromacs.org
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> > > >Please don't post (un)subscribe requests to the list. Use the
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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
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
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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
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >_______________________________________________
> >gmx-users mailing list
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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
>
>
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
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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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