[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC
science at louic.nl
Mon Sep 12 10:59:33 CEST 2005
I think I (finally :-) solved the problem with the popc bilayers
separating. The clue appeared to be in Andrey Golovin's answer (thanks
It looks like the water density in the popc file from Dr. Tieleman's
website is lower than the water densities in his dppc and dmpc files
(contrary to my previous message, sorry). After removing all the water
from the popc128a.pdb file, rehydrating (genbox), and removing the water
it placed inside the bilayer, the leaflets did not separate anymore.
For those who are interested, I put some data from g_density on my
website: http://www.louic.nl/temp/bilayers.png (it will stay there for a
couple of weeks).
Thanks everybody for your cooperation!
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.
> 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, 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. As far as I know, these lipids
>> do not differ that much. I did not (yet) modify any of the files
>> 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".
>> 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
>>  http://moose.bio.ucalgary.ca/index.php?page=Downloads
>>  .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
>>  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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