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

[Louic Vermeer]

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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> 
>