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

[Xavier Periole]

Dear Jian,

I do not see anything especially wrong in your file except may be the
pressure stuff. Try the following parameters. Your compressibility is
pretty low. That might be it.

tau_p                    = 1.20 1.20
compressibility          = 5e-5 5e-5
ref_p                    = 1.0  1.0

One other thing. In the CG FF the time step is considered as part of the
force field. Meaning that you should not play with it too much.
0.04-0.02 ps is the actual range where the force field is considered
to reproduce experimental values of various quantities used for
paraameterization of the FF. Outside this range you change the balance
between the different terms and thus would alter the quality of the FF.

XAvier
PS: I send the email to the gmx-users list. Other people might be
interested bu the answer.

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
-----------------------------------------------------