[gmx-users] Area compressibility modulus GMX
John Whittaker
johnwhittake at zedat.fu-berlin.de
Tue Dec 11 18:23:15 CET 2018
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
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