[gmx-users] Area compressibility modulus GMX
pbuscemi at q.com
Thu Dec 13 02:50:32 CET 2018
Ain’t nothin’ silly about analyzing membranes. It’s an artform .
Have you taken a look at Membplugin https://sourceforge.net/p/membplugin/wiki/Home/ <https://sourceforge.net/p/membplugin/wiki/Home/> it provides trajectory values for among other things thickness and area/lipid.
I’ve not read the paper but the “average of the squared fluctuation” certainly has the appearance of a variance. Your procedure seems reasonable just check from the lit that the DPPC values reach those found at equilibrium. In my simulations of DPPC a 250x250 sq Ang bilaer took ~ 100ns far longer than I initially expected.
> On Dec 11, 2018, at 11:23 AM, John Whittaker <johnwhittake at zedat.fu-berlin.de> wrote:
> 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!
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