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
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Received on Mon Aug 01 2016 - 12:30:02 PDT
