[gmx-users] Re: abnormal flip-flop when embedding cholesterol into DOPC using CG

Xavier Periole X.Periole at rug.nl
Thu Dec 6 13:39:27 CET 2007


Regarding the flip-flop. I just talk to Siewert-Jan Marrink. They
got a paper just accepted in JACS as a communication which describes
the time scale of cholesterol flip-flopping in membrane bilayers as
found with the MARTINI CG. Very nice paper. It should get out in the
ASAP section pretty soon (DOI:10.1021/ja076641c).

In summary the cholesterol flip flop time ranges from 0.1 to 4.5 micro
seconds depending on the membrane bilayer. The concentration in cholesterol
is also important: the more cholesterol the less flip flop.

You could position restrain your cholesterol molecules and equilibrate
the lipids before letting everything free. I would also suggest to
couple lipid and chol to the same T bath.

XAvier

On Wed, 5 Dec 2007 17:17:17 -0500
  "Jian Dai" <djpittdj at gmail.com> wrote:
> Hi, XAvier:
> Thank you for your reply on the GMX mailing-list.
> As a matter of fact, I didn't change much of the run parameters provided in
> the example section from the MARTINI's website
> except changing timestep from 0.04 to 0.02 and coupling DOPC and CHOL
> together to the thermostat. And the parameter I use is like the
> following.
> 
> Thank you anyway.
> -dj
> 
> 
> title = Martini
> cpp = /usr/bin/cpp
> integrator = md
> tinit = 0.0
> dt = 0.02
> nsteps = 20000000 ;normal value 50000
> nstcomm = 1
> comm-grps = DOPC CHOL W
> nstxout = 50000
> nstvout = 50000
> nstfout = 0
> nstlog = 1000000
> nstenergy = 1000
> nstxtcout = 10000
> xtc_precision = 100
> xtc-grps =
> energygrps = DOPC CHOL W
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.2
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r = 15
> vdw_type = Shift
> rvdw_switch = 0.9
> rvdw = 1.2
> DispCorr = No
> tcoupl = Berendsen
> tc-grps = DOPC_CHOL W
> tau_t = 1 1
> ref_t = 310 310
> Pcoupl = berendsen
> Pcoupltype = semiisotropic
> tau_p = 2 2
> compressibility = 1e-5 1e-5
> ref_p = 1.0 1.0
> gen_vel = yes
> gen_temp = 105
> gen_seed = 473529
> constraints = none
> constraint_algorithm = Lincs
> unconstrained_start = no
> lincs_order = 4
> lincs_warnangle = 30
> 
> ----------------------------------------------------------------------------------------------------------------------------------------------
> 
> Hi,
> 
> This does not look right indeed. You should give more details about your
> simulations parameters: Pcoupling, T, compressibility, [chol], bix size,
> time step ...
> 
> XAvier
> 
>> Hi, all:
>> I'm trying to embed cholesterol molecules into a DOPC bilayer in a coarse
>> grained model.
>> The force field and coordinates for a pure DOPC bilayer and for
> cholesterol
>> were obtained on the MARTINI's site. I randomly replace a DOPC molecule
> with
>> a cholesterol molecule and do the energy minimization. After embedded a
>> certain amount of cholesterols, I run the simulation by coupling DOPC and
>> CHOL together to a thermostat. However, the cholesterols turn to be very
>> unstable and flip-flop a lot between the monolayers, which I think is not
>> expected.
>> Any suggestions will be greatly appreciated.Thank you.
>> dj
> 
> -----------------------------------------------------
> XAvier Periole - PhD
> 
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> ----------------------------------------------------

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------



More information about the gromacs.org_gmx-users mailing list