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

Wed Sep 12 19:41:41 CEST 2012

Hi,

While comparing to other simulations can be useful, I would argue that 
the real test for the combination of force field and simulation 
parameters is to determine if the simulated membrane properties compare 
well to the experimentally determined values. As long as they do this, 
you can argue that your choices are sensible. Obviously if you are 
including proteins (or other molecules) in the system, the parameters 
need to also be shown to work well for these too.

As for not including the dispersion correction, yes it is fine to do 
this (if it improves the behaviour of your membrane) as a dispersion 
correction is most appropriately applied to homogeneous systems and not 
membranes.

Regarding the large range of values seen, I would only be concerned if 
you are exactly reproducing what other people have done, in terms of 
force field and simulation parameters used and seeing large differences 
to what they report. As I mentioned before, fairly small changes in some 
of these parameters can make some pretty substantial impacts upon the 
membrane properties. You also should be careful to ensure that the 
properties of the membranes you are analysing are converged (a block 
analysis is the way to properly check this).

Cheers

Tom

On 12/09/12 18:21, David Ackerman wrote:
> Hi,
>
> Thank you for your response. As to my concern about incorrect areas
> and diffusion, I am basing it off of other papers that simulate DPPC
> bilayers.
>
> For instance, in this paper:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251217/figure/F12/ , they
> simulate a DPPC bilayer with DiI molecules in it. I did the same
> simulation, but whereas they get APL of ~.64-.65 nm^2, mine are again
> ~0.03-0.04 nm^2 smaller. Also, in this paper they show that the lipids
> diffuse ~1.1 nm^2 over the span of 20 ns, whereas I get a much slower
> rate of traveling ~1.4-1.6 nm^2 over 90 ns. As mentioned in the other
> response, if I turn off dispersion correction I get higher APL
> (~.65-.66 nm^2) and diffusion values that more closely match this and
> other papers.
>
> These APLs and diffusion values are similar for some other papers that
> simulate DPPC bilayers.
>
> Is it ok to have ranges this large compared to these other
> simulations, and does it make physical sense to turn off the
> dispersion correction for this force field?
>
> Thanks for your time,
> David
>
> On Wed, Sep 12, 2012 at 11:29 AM, Justin Lemkul <jalemkul at vt.edu> 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
>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
Dr Thomas Piggot
University of Southampton, UK.