[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC
David L. Bostick
dbostick at physics.unc.edu
Fri Sep 9 19:24:01 CEST 2005
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
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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
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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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