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

[Thomas Piggot]

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.