[AMBER] Calculating lipid diffusion using stfcdiffusion

From: Amy Rice <arice3.hawk.iit.edu>
Date: Thu, 7 Jul 2016 12:49:07 -0500

Hi all,
I am attempting to calculate the diffusion coefficient for a lipid based on
a 1500 ns bilayer simulation that I performed, but I am a little confused
by the output that I'm receiving from stfcdiffusion in cpptraj. I am using
AmberTools 16, and have attached my cpptraj input scripts to show exactly
what I am doing in each case.

This is the procedure I've been using: first, I unwrap my trajectory, then
center one of the leaflets at the origin using "center .1-16740 mass
origin" (here, atoms 1-16740 correspond to the top leaflet). After this, I
calculate the MSD using "stfcdiffusion mask .1-16740 out diffusion_top.dat
time 100 xy". When I plot the MSD in xy with time, it has the general shape
I would expect (see the attached figure LPS_top.pdf), and the diffusion
coefficient that I calculate from it matches the experimental value.
However, when I go back and do the exact same procedure, using now the
bottom leaflet as my atom mask, the plot does not behave as I would expect.
First, the xy MSD starts at ~ 1100 instead of 0, and then decreases with
time (see the attached figure LPS_bottom.pdf). Finally, if I use the full
bilayer as my atom mask, the plot starts at 0 but has large fluctuations
where it increases rapidly then decreases rapidly (figure LPS_all.pdf). I'm
at a bit of a loss to explain this behavior, because if I visualize the
unwrapped, centered trajectories, the appropriate portion of the bilayer is
centered and no strange imaging issues seem to be occurring.

As a test, I repeated these same calculations using a bilayer simulation of
a similar lipid, and have the same type of results where the top leaflet
results in a nice plot and a reasonable diffusion coefficient, whereas
using the bottom leaflet gives a plot that starts large and decreases, and
using both leaflets has large fluctuations and is non-linear (figures
mLPS_top.pdf, mLPS_bot.pdf, and mLPS_all.pdf).

Is this behavior expected? I tried following the link given in the Amber 16
manual to learn more about the diffusion routine developed by Hannes
Loeffler that stfcdiffusion is based off but was unable to locate any
pertinent documentation or publications. The data from the top leaflet
seems usable, but I would like to be able to average over both leaflets if
possible so that I am including more lipids and can get a better estimate
of the diffusion coefficients.

Thank you,
- Amy

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology

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Received on Thu Jul 07 2016 - 11:00:03 PDT
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