[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC

[Andrey V. Golovin]

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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Andrey V. Golovin
Ph.D,Professor assistant    tel: (095) 939-5305
Bioengineering and
Bioinformatics Department
Moscow State University     fax: (095) 939-3181
119899 Moscow            E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su
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