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" <[EMAIL PROTECTED]> 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
-----------------------------------------------------
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