On 10/31/18 2:25 PM, ABEL Stephane wrote:
Just my 2 cents If I recall well CHARMM36 and others force fields (such as lipid14) were initially parametrized and validated using the anisotropic pressure
True, but only for a few tens of nanoseconds in the case of C36. The pressure coupling specification is not strictly tied to the force field.
coupling scheme. So it make sense to use it instead of semi-isotropic pressure coupling. Moreover I found that if the membrane system is well equilibrated (for instance > 100 ns of NPT is semiisotropic for POPC or DOPC membranes), you can switch safely to anistropic pressure scheme and does not observe significant deformations of the bilayer. These observations are based on my simulations and are of course not general?
Anisotropic coupling doesn't make sense to me for membranes (though it was used routinely years ago, as you note). The lateral properties of a membrane are not different in x and y (assuming the bilayer normal is along z, per convention). Hence, semiisotropic coupling is the most defensible. I have seen simulations of less than 100 ns distort quite a bit, though the importance of such behavior (square becoming a rectangle, but everything still satisfying the minimum image convention) is not clear.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
