Hi all, I have a weird, probably very basic question to ask and I hope it is appropriate for the mailing list.
I am trying to reproduce the pure DPPC bilayer data found in J. Chem. Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using the recommended protocol given in the paper. I have calculated the area per lipid for my system and have an average value and am now attempting to calculate the area compressibility modulus, K, using the formula given in the paper in the subsection "Analysis" (which itself is taken from https://doi.org/10.1063/1.479313). I am a bit confused by the wording when the authors describe the value in the denominator, <delta_A^2>. The paper calls this value "the average of the squared fluctuation of the area/lipid". I'm probably being silly, but am I right to assume that this is the variance of the area/lipid? As in, to get this value I can: 1) Use gmx analyze to find the standard deviation of the area/lipid over the course of my trajectory 2) Square the standard deviation to find the variance of the area/lipid Then, it's a straightforward process of plugging in and making sure everything comes out in dyn/cm. Could anyone tell me if my process is correct? Thanks a lot and my apologies if this is too specific of a question for the mailing list! John -- 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.