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

David Ackerman da294 at cornell.edu
Wed Sep 12 20:07:16 CEST 2012


Right I guess my biggest concern was diffusion. I did in fact do 12
simulations of DPPC bilayers for 100 ns each, and still got the
aforementioned APL and diffusion. When I turn off the dispersion, I
get more appropriate APL and MSD values, that match other papers, even
when only looking at one simulation. To me, it does not seem the mdp
file I used is able to get more common APL and diffusion values even
when averaging over a large number of simulations.

As for the pressure in the x/y direction, is it more appropriate to
use 1 atm or 0 atm for bilayer simulations?


On Wed, Sep 12, 2012 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 9/12/12 1:21 PM, 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.
> The paper cited above does not report any error estimates for their values
> (unless I have missed them) and it appears they produced only one trajectory
> per condition.  Multiple simulations and proper statistical measurements
> should be made.  Experimental ranges for DPPC APL (if I recall them
> properly) are 0.62-0.65 nm^2 at 323K, so everyone seems to be in the right
> ballpark.
> Regarding diffusion, that's harder to compare.  You're also seeing less
> diffusion than in Lindahl and Edholm (2001) J. Chem. Phys. 10: 4938-4950
> over the same time period (MSD there was on the order of 4 nm^2 by 90 ns).
>> 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?
> I think it all amounts to sampling.  One trajectory is not definitive.
> Averaging over several that have been demonstrated to have converged is much
> more reliable.  Lipids take a long time to be happy; 20-40 ns of
> equilibration time may have to be neglected before claiming "equilibrium"
> properties.
> -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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