Re: [AMBER] Calculating lipid diffusion using stfcdiffusion

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 26 Jul 2016 13:53:14 -0600

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
>>> > 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
```
Received on Tue Jul 26 2016 - 13:00:02 PDT
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