# Re: [AMBER] Calculating lipid diffusion using stfcdiffusion

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 1 Aug 2016 13:24:37 -0600

Hi,

Remember that the output for 'out' is mean squared displacement vs
time (see the manual), so the values are already squared. So if you
sum the X (which is really x^2) and Y (which is y^2), you get the xy
column (x^2 + y^2). Does this make sense?

-Dan

On Mon, Aug 1, 2016 at 1:06 PM, Amy Rice <arice3.hawk.iit.edu> wrote:
> Hi Dan,
> Sorry for the delayed response! I repeated the calculation using the github
> version of cpptraj, and that seems to have fixed the issues I was having
> with the second leaflet. Now the MSD starts at 0 and evolves with time as
> expected. However, I noticed that the MSD in XY is not equal to sqrt(X^2 +
> Y^2) in the output (example below). Is the XY MSD calculated differently
> than sqrt(X^2 + Y^2) when using stfcdiffusion? I tried looking into the
> source code (Action_STFC_Diffusion.cpp) to see how exactly it is
> calculated, but my knowledge of C++ is very limited...
> Thank you again for the help!
>
>
> Portion of the stfcdiffusion output:
> #time x y z xy
> 100.000 1.463 1.361 0.884 2.824
> 200.000 1.743 1.801 1.206 3.545
> 300.000 2.125 1.975 1.331 4.100
>
>
> On Thu, Jul 28, 2016 at 3:21 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> There was in fact a bug in the 'stfcdiffusion' command when using the
>> standard calculation mode (i.e. not center of mass or with a second
>> mask) when the first atom mask selection did not start at one - this
>> is probably why the results for the second leaflet were bad with
>> 'stfcdiffusion'. If you get a chance, could you try repeating the
>> calculation with the GitHub version of cpptraj
>> (http://github.com/Amber-MD/cpptraj)? I will also be preparing a patch
>> for AmberTools.
>>
>> Thanks for the report,
>>
>> -Dan
>>
>> PS - I want to mention that this bug is my fault (not Hannes') and is
>> not present in the original modified ptraj version of this command.
>>
>> On Tue, Jul 26, 2016 at 1:53 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> > Hi,
>> >
>> > It seems like there may be a bug in the 'stfcdiffusion' command. I am
>> > going to look into it and report back.
>> >
>> > -Dan
>> >
>> > On Wed, Jul 20, 2016 at 12:57 PM, Amy Rice <arice3.hawk.iit.edu> wrote:
>> >> Sorry to reply again so quickly, but there is something else I just
>> noticed
>> >> about the output from stfcdiffusion. As I mentioned above, I believe
>> MSD in
>> >> xy should be calculated as sqrt(X^2 + Y^2) (please correct me if I am
>> >> wrong!!). However, the xy MSD in the output from stfcdiffusion is not
>> the
>> >> same as what I calculate it should be, based on the x and y MSDs
>> written to
>> >> the output file. Attached, I've plotted MSD using the xy result and the
>> MSD
>> >> using sqrt(x*x+y*y). The two clearly don't match. However, the MSD using
>> >> sqrt(x*x+y*y) with the stfcdiffusion output matches perfectly the output
>> >> from 'diffusion'. In other words, diffusion and stfcdiffusion agree
>> >> perfectly when they calculate the x and y MSDs, it is just that the
>> >> stfcdiffusion xy MSD does not match sqrt(x^2+y^2). I hope I am
>> explaining
>> >> this in a way that makes sense!
>> >> Below, I have included some portions of the output from stfcdiffusion,
>> >> using the top leaflet of my LPS bilayer system. Am I misunderstanding
>> how
>> >> stfcdiffusion calculates the xy MSD or is there something else going on
>> >> here?
>> >>
>> >>
>> >> ####################################
>> >> #time x y z xy
>> >> 100.000 1.463 1.361 0.884 2.824
>> >> 200.000 1.743 1.801 1.206 3.545
>> >> 300.000 2.125 1.975 1.331 4.100
>> >> 400.000 2.172 2.290 1.405 4.462
>> >> 500.000 2.540 2.469 1.430 5.009
>> >> 600.000 2.529 2.621 1.496 5.150
>> >> 700.000 2.775 2.744 1.608 5.519
>> >> [...]
>> >> 759100.000 14.611 15.105 6.255 29.716
>> >> 759200.000 14.636 15.450 6.124 30.086
>> >> 759300.000 14.774 15.283 5.919 30.057
>> >> 759400.000 14.486 15.232 6.009 29.718
>> >> 759500.000 14.634 15.158 6.145 29.793
>> >> 759600.000 14.554 15.131 5.664 29.686
>> >> 759700.000 15.075 15.811 6.089 30.886
>> >> 759800.000 14.838 15.277 5.548 30.115
>> >> 759900.000 14.750 15.661 5.751 30.411
>> >> 760000.000 14.519 15.309 5.383 29.828
>> >> 760100.000 14.959 15.787 5.795 30.745
>> >> 760200.000 14.771 15.825 6.015 30.596
>> >> 760300.000 15.300 15.818 5.735 31.118
>> >> 760400.000 14.885 16.014 6.068 30.899
>> >> 760500.000 15.090 15.375 5.983 30.465
>> >> [...]
>> >> 1497900.000 16.380 16.944 7.148 33.324
>> >> 1498000.000 15.848 16.386 6.894 32.234
>> >> 1498100.000 16.048 16.246 7.261 32.295
>> >> 1498200.000 16.097 16.529 7.385 32.626
>> >> 1498300.000 16.226 16.498 7.298 32.724
>> >> 1498400.000 16.553 17.061 7.175 33.614
>> >> 1498500.000 16.119 16.694 7.823 32.813
>> >> 1498600.000 16.538 16.925 7.840 33.464
>> >> 1498700.000 16.112 16.480 7.824 32.591
>> >> 1498800.000 16.378 15.839 7.585 32.217
>> >> 1498900.000 16.629 15.982 7.637 32.611
>> >> 1499000.000 16.595 15.833 7.688 32.428
>> >> 1499100.000 17.022 15.900 7.549 32.921
>> >> 1499200.000 17.061 15.925 7.964 32.987
>> >> 1499300.000 16.638 15.984 7.585 32.622
>> >> 1499400.000 16.829 16.049 8.463 32.878
>> >> 1499500.000 16.473 15.913 7.610 32.386
>> >> 1499600.000 16.968 16.213 7.663 33.182
>> >> 1499700.000 16.372 16.421 7.631 32.793
>> >> 1499800.000 16.211 16.946 7.495 33.157
>> >> 1499900.000 16.485 16.430 7.782 32.915
>> >>
>> >>
>> >>
>> >>
>> >> On Wed, Jul 20, 2016 at 1:34 PM, Amy Rice <arice3.hawk.iit.edu> wrote:
>> >>
>> >>> Hi Callum and Dan,
>> >>> Thank you both for getting back to me!
>> >>>
>> >>> I have gone back and tried using the "diffusion" routine. For this, I
>> use
>> >>> the exact same cpptraj input as above, except instead of the
>> >>> 'stfcdiffusion' line, I use 'diffusion mask .1-16740 out
>> diffusion_top.dat
>> >>> time 100 noimage'. The plotted MSD in xy is calculated as: sqrt(X^2 +
>> Y^2),
>> >>> which I believe should be the correct way to determine it. As you can
>> see,
>> >>> when using the top leaflet both diffusion and stfcdiffusion result in
>> >>> similar, but slightly different plots (see the attached figure
>> >>> LPS_comparison.pdf); the diffusion coefficient I calculate from them
>> is 1.3
>> >>> x10^(-10) cm^2/s and 1.9 x10^(-10) cm^2/s, respectively. However,
>> diffusion
>> >>> and stfcdiffusion produce very different plots for the bottom leaflet.
>> The
>> >>> diffusion routine gives the general shape that I would expect, and very
>> >>> similar to what I see when using the top leaflet. I'm not sure why
>> >>> stfcdiffusion gives something wildly different for the bottom leaflet.
>> This
>> >>> diffusion/stfcdiffusion difference is consistent for both of my bilayer
>> >>> systems (mLPS_comparison.pdf, attached).
>> >>>
>> >>> As far as my thought process behind centering the trajectory after I
>> >>> unwrap it- I found that this step is necessary for two reasons. First,
>> the
>> >>> two leaflets of the bilayer have a tendency to "caterpillar" across
>> each
>> >>> other, meaning they have COM motion relative to each other. I believe
>> this
>> >>> is part of the problem I'm having when I use 'stfcdiffusion' on the
>> full
>> >>> bilayer, which is why I started looking at the individual leaflets
>> >>> The second reason I center the trajectory is that the simulation box
>> itself
>> >>> seems to move around with respect to the origin. What I mean is that,
>> if I
>> >>> visualize the unwrapped trajectory in VMD, the bilayer patch floats
>> around
>> >>> seemingly at random in x, y, and z. I agree that it seems like I
>> should be
>> >>> able to calculate diffusion from the unwrapped system directly, but in
>> >>> practice this gives MSD plots that don't really make sense (see the
>> >>> attached *_nocenter.pdf for example- these were made using the exact
>> same
>> >>> commands as before, just with commenting out the 'center' step). This
>> >>> behavior occurs in both of my bilayer systems, though I'm not entirely
>> sure
>> >>> why the box moves around like this.
>> >>>
>> >>> Thank you,
>> >>> Amy
>> >>>
>> >>> On Tue, Jul 19, 2016 at 10:26 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> >>> wrote:
>> >>>
>> >>>> Hi,
>> >>>>
>> >>>> On Thu, Jul 7, 2016 at 11:49 AM, Amy Rice <arice3.hawk.iit.edu>
>> 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?
>> >>>>
>> >>>> -Dan
>> >>>>
>> >>>> > 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
>> >>>> > 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
>> >>>> > AMBER.ambermd.org
>> >>>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>>> >
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>> -------------------------
>> >>>> Daniel R. Roe, PhD
>> >>>> Department of Medicinal Chemistry
>> >>>> University of Utah
>> >>>> 30 South 2000 East, Room 307
>> >>>> Salt Lake City, UT 84112-5820
>> >>>> http://home.chpc.utah.edu/~cheatham/
>> >>>> (801) 587-9652
>> >>>> (801) 585-6208 (Fax)
>> >>>>
>> >>>> _______________________________________________
>> >>>> AMBER mailing list
>> >>>> AMBER.ambermd.org
>> >>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Amy Rice
>> >>> Ph.D. Student
>> >>> Physics Department
>> >>> Illinois Institute of Technology
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> Amy Rice
>> >> Ph.D. Student
>> >> Physics Department
>> >> Illinois Institute of Technology
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

```--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
```
Received on Mon Aug 01 2016 - 12:30:03 PDT
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