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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
*

*>> instead.
*

*>> >>> 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
*

*>> >>>> > 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
*

*>> >>>> > 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
*

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:

-- ------------------------- 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/amberReceived on Mon Aug 01 2016 - 12:30:03 PDT

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