[gmx-users] Smaller Area Per Lipid for DPPC Bilayer
chris.neale at mail.utoronto.ca
Wed Sep 12 20:30:40 CEST 2012
While dispersion correction is a great idea that helps to reduce the impact of the precise choice of cutoff distance on the results, the Berger parameters (and indeed all other parameters) were not developed with the inclusion of dispersion correction and one could argue that it is thus non-optimal to include dispersion correction here... especially since it leads to poorer results.
This is separate from the difference between isotropic dispersion correction and a proper "PME"-type LJ term. Both of which are expected to lead to smaller APLs.
When using anisotropic pressure coupling for lipid bilayers, you should use 1 atm in all dimensions.
-- original message --
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?
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