Hello, 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 On Wed, Sep 12, 2012 at 1:43 PM, Justin Lemkul <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
