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

Justin Lemkul jalemkul at vt.edu
Wed Sep 12 19:43:22 CEST 2012

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


More information about the gromacs.org_gmx-users mailing list