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From: Amy Rice <arice3.hawk.iit.edu>

Date: Mon, 1 Aug 2016 14:35:03 -0500

Ah, yes I see that now. Thank you for clearing that up for me!

On Mon, Aug 1, 2016 at 2:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

*> 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
*

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> 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
*

*>
*

Date: Mon, 1 Aug 2016 14:35:03 -0500

Ah, yes I see that now. Thank you for clearing that up for me!

On Mon, Aug 1, 2016 at 2:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

-- Amy Rice Ph.D. Student Physics Department Illinois Institute of Technology _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Aug 01 2016 - 13:00:02 PDT

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