[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC
Andrey V. Golovin
golovin at genebee.msu.su
Mon Sep 12 11:04:15 CEST 2005
will meet you in Wageningen soon =)
Louic Vermeer wrote:
> Hi everybody!
> I think I (finally :-) solved the problem with the popc bilayers
> separating. The clue appeared to be in Andrey Golovin's answer (thanks
> again Andrey!).
> 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
>> 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
>>> - 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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Andrey V. Golovin
Ph.D,Professor assistant tel: (095) 939-5305
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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