# Re: [AMBER] Calculating lipid diffusion using stfcdiffusion

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
> >> >>> 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
> 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
>

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