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