[AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Tue, 03 Oct 2017 17:52:41 +0200


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
at 303 K.


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:


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

   Thank you in advance,

       Best wishes,


************************ production MD input file *********
************************ production MD input file *********
************************ production MD input file *********

   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,

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Received on Tue Oct 03 2017 - 09:00:01 PDT
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