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

[Andrey V. Golovin]

Hi Louic!
welcome :)
will meet you in Wageningen soon =)

Andrey


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!
> 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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-- 
-----------------------------------------------------------------
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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