[gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Justin Lemkul jalemkul at vt.edu
Wed Sep 12 17:29:33 CEST 2012

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 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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