Hi Marek,
Based on area per lipid values, it looks like DPPG is no longer in liquid-disordered phase. If I remember correctly, the transition temperature for DPPG is around 313K, and for POPG is 269K. Are you sure that DPPG is in l-o phase at 303K?
Best,
Batuhan
> On 3 Oct 2017, at 17:52, Marek Maly <marek.maly.ujep.cz> wrote:
>
> Hello,
>
> I have question regarding DPPG bilayer simulation.
>
> I recently simulated DPPG and also (as the "control") POPG (which is quite
> similar lipid) lipid bilayer.
>
> Here you can see evolution of the area per lipid during the 400 ns MD
> simulation
> at 303 K.
>
> http://physics.ujep.cz/~mmaly/lipids/
>
> The production MD input file is at the end of this email. The setup for
> all simulation phases was
> similar to the one used in the relevant tutorial:
>
> http://ambermd.org/tutorials/advanced/tutorial16/
>
> The lipid bilayers were constructed using CHARMM Membrane Builder.
> Hydration: 50 H2O molecules per lipid
> Neutralization: 128 lipids/128 lipids bilayer was neutralized using 256
> Na+ ions.
> Lipid17 ff was used and TIP3P water.
> For Na+ ions were used older ff99 parameters as recommended in Amber Lipid
> 14 article (Phys.Chem.Chem.Phys., 2016, 18, 10573) to be closer no-salt or
> low-concentration-salt experimental
> conditions - i.e. to prevent stronger condensation of the anionic lipids.
>
> As we can see in the above mentioned figure, DPPG area per lipid has
> significantly decreased
> from the initial 62.7 A^2 to ca 49.9 A^2 while in POPG case the area just
> little increased from the initial 62.27 A^2 to ca 66.4 A^2 which is in
> quite good agreement with the simulation and experimental result from the
> above mentioned Amber article (MD Lipid14 66.7, experiment 64.3 or 66.1).
>
> So my question is simple. Could be the results obtained for DPPG
> sufficiently realistic in spite of that rather small (in comparison to
> similar POPG or to the initial area estimate) final area per lipid ?
>
> It is not so easy to find experimental results for pure DPPG in water,
> neutral pH... so I would appreciate some eventual tips and relevant
> comments.
>
> Thank you in advance,
>
> Best wishes,
>
> Marek
>
>
> ************************ production MD input file *********
> ************************ production MD input file *********
> ************************ production MD input file *********
>
>
> &cntrl
> imin=0, ! Molecular dynamics
> ntx=5, ! Positions and velocities read formatted
> irest=1, ! Restart calculation
> ntc=2, ! SHAKE on for bonds with hydrogen
> ntf=2, ! No force evaluation for bonds with hydrogen
> tol=0.0000001, ! SHAKE tolerance
> nstlim=250000, ! Number of MD steps
> ntt=3, ! Langevin thermostat
> gamma_ln=1.0, ! Collision frequency for thermostat
> temp0=303.0, ! Simulation temperature (K)
> ntpr=5000, ! Print to mdout every ntpr steps
> ntwr=50000, ! Write a restart file every ntwr steps
> ntwx=249000, ! Write to trajectory file every ntwc steps
> dt=0.002, ! Timestep (ps)
> ig=-1, ! Random seed for Langevin thermostat
> ntb=2, ! Constant pressure periodic boundary conditions
> ntp=2, ! Anisotropic pressure coupling
> cut=10.0, ! Nonbonded cutoff (Angstroms)
> ioutfm=1, ! Write binary NetCDF trajectory
> ntxo=2, ! Write binary restart file
> ! iwrap=1,
> /
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/
>
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Received on Wed Oct 04 2017 - 12:00:03 PDT
