Hi,
The experimental range of diffusion coefficients are quite large for
DPPC, plus the force field and simulation parameters can have a large
impact upon the diffusion speeds seen in the simulations. We have just
published a study comparing force fields for simulating DPPC and POPC
membranes and further details on differences in lipid diffusion are
provided in the paper:
http://pubs.acs.org/doi/abs/10.1021/ct3003157
We did not test this exact set of cut-offs with this force field.
However, from the tests we did perform using these Berger DPPC
parameters, I expect that the diffusion speeds should fall within the
experimental range using this set of cut-offs. As for the area per
lipid, what you are seeing is pretty much as I would expect with the 1.2
nm cut-offs and a dispersion correction. If you want a higher area per
lipid, you could try removing the dispersion correction or reducing the
cut-off (with the dispersion correction, we saw sensible membrane
behaviour with 1.0 nm cut-offs). Do be sure to check the lipid diffusion
rate is still sensible if you remove the dispersion correction, as it
should substantially increase when doing this (see the paper for some
more details).
Cheers
Tom
On 12/09/12 16:29, Justin Lemkul wrote:
On 9/12/12 10:56 AM, David Ackerman wrote:
Hello,
I have been basing some DPPC bilayer simulations off of files from
Justin Lemkul's tutorial, including the .itp files and .mdp files.
Everything has been working fine except that my area/lipid seems to be
too low and my diffusion coefficient seems to be too slow compared to
experimental values. As a test, I just started with Tieleman's
How far off are the diffusion constants? I have never had a lot of
luck reproducing experimental values, but this may reflect a
limitation of the parameter set, simulation length, or both.
equilibrated 128 DPPC bilayer system, including the waters, and ran a
simulation using the mdp file below (note though I selected
continuation=yes, this was in fact not continued from a previous
equilibration). The simulation has been running for ~75 ns so far, and
the area/lipid is on average ~.61-.62 nm^2 . When I do full
That sounds like the expected outcome for this force field. Why do
you say that is too low?
temperature/pressure equilibrations, even using different
thermostats/barostats, I seem to get area/lipid values similar to
these. Also, my diffusion coefficients are smaller than those reported
in papers invovling DPPC bilayers. I was wondering what the possible
reasons for this could be. Any help you could provide would be great.
Curiosities in the .mdp file:
tcoupl = Nose-Hoover ; Less accurate thermostat
tc-grps = DPPC SOL ; three coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 323 323 ; reference temperature, one for each
Why is your tau_t so small? Generally one should use 0.5 - 2.0 with
Nose-Hoover.
group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box
vectors, independent z
tau_p = 1.0 ; time constant, in ps
ref_p = 0.0 1.0 ; reference pressure, x-y, z
(in bar)
Why are you setting zero pressure along the x-y plane?
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility,
bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
If you are not continuing from a previous run (as you say above) and
you are also not generating velocities, you may be delaying
equilibration by allowing the initial forces dictate the velocities.
I suppose if the run is stable enough, this is not a huge problem, but
in general this combination is not recommended.
-Justin
--
Dr Thomas Piggot
University of Southampton, UK.
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