Thanks a lot Batuhan, that will be the point !
Best wishes,
Marek
Dne Wed, 04 Oct 2017 20:41:43 +0200 Batuhan Kav <bkav13.ku.edu.tr>
napsal/-a:
> 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 - 17:00:03 PDT
