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. Chris. -- 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? -David -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
