Re: [AMBER] Calculating lipid diffusion using stfcdiffusion

From: Dickson, Callum J <>
Date: Mon, 18 Jul 2016 20:25:17 +0000

Hi Amy,

For consistency, have you checked to see if you get the same results using the older "diffusion" routine from ptraj.mod ?



From: Amy Rice <>
Sent: Thursday, July 14, 2016 12:13:57 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Calculating lipid diffusion using stfcdiffusion

Hi all,
Can anyone offer insight into this strange/unexpected behavior that I am
seeing? I thought initially the issue was with my bilayer imaging, but the
imaged trajectories visually look correct and do not display any weird
jumping or drifting that I can see. Any feedback would be greatly

On Thu, Jul 7, 2016 at 12:49 PM, Amy Rice <> wrote:

> 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

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Mon Jul 18 2016 - 13:30:02 PDT
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