Re: [AMBER] Calculating lipid diffusion using stfcdiffusion

From: Daniel Roe <>
Date: Tue, 19 Jul 2016 09:26:01 -0600


On Thu, Jul 7, 2016 at 11:49 AM, Amy Rice <> wrote:
> 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.

I guess I'm not clear on why you are performing 'center' after you
'unwrap'. To me, the point of a diffusion calculation is to determine
the rate of free motion of molecules in your system. By adding the
'center' command, you're artificially changing that motion. Why
wouldn't you just calculate diffusion for the unwrapped system itself?


> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Tue Jul 19 2016 - 08:30:04 PDT
Custom Search