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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

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

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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