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

Louic Vermeer science at louic.nl
Wed Sep 7 15:32:41 CEST 2005

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) 

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".

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


[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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