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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