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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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