# Re: [AMBER] PCA: comparing PCs from different trajectories

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 6 Aug 2015 14:06:45 -0600

On Thu, Aug 6, 2015 at 8:18 AM, George Tzotzos <gtzotzos.me.com> wrote:
> kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name PC1-PC2-1
>
> 1. Does the produced histogram (see attached) represent the Kullback−Leibler divergence of the first 5 PCs between run 1 and 2? Is this correct?

There was no attachment (maybe try sending it to me directly?), but if
you are referring to KL-PC.agr this should contain the time dependent
Kullback-Leibler divergence (i.e. calculating the KL divergence as
histograms are populated) for the first 5 PCs.

> 2. In the affirmative, I guess I should do the same for run 1 and 3, 1 and 4, etc. Am I right?

Sure, if you want to see how converged the PC projection distributions
are for those runs :-).

> 3. Last but not least, I don’t see anywhere in the output how much of the total motion is represented in the 1st, 2nd and 3rd PC for each run. Is there a way to produce this type of output?

Check out the analysis command 'modes' and keyword 'eigenval'. The
input would look something like this assuming evecs.dat contains
previously generated eigenmodes:

modes name evecs eigenval out eigenval.dat

Hope this helps,

-Dan

>
> Once again thank you for your kind help
>
> Regards
>
> George
>
>
>
>
>> On 5 Aug 2015, at 21:18, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> On Wed, Aug 5, 2015 at 11:39 AM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>>> crdaction crd1 projection T1 modes evecs.dat beg 1 end 20 :1-125&!.H= \
>>> crdframes 1, 2000 out T1.dat
>>
>> Remove the space in your crdframes argument, e.g. 'crdframes 1,2000'.
>> This is the source of your error messages.
>>
>>> Warning: No actions/output trajectories specified.
>>
>> This is because you only have analyses set up at the end (kde etc).
>> Can be safely ignored.
>>
>>> Warning: Size of Mode1 (10000) != size of Mode1 (8000)
>>> Warning: Only using 8000 data points.
>>
>> This is related to your malformed crdframes arguments above - each
>> projection start argument was read but not the end because of the
>> space. So the first projection T1 had 10000 frames, the second 8000,
>> and so on. This will be resolved after you fix the crdframes
>> arguments.
>>
>> Hope this helps,
>>
>> -Dan
>>
>>>
>>>
>>>
>>>
>>>> On 5 Aug 2015, at 20:16, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> This is by no means the only way, but we've done this kind of analysis
>>>> recently (see http://pubs.acs.org/doi/abs/10.1021/jp4125099). The idea
>>>> is to calculate principal components from a combined trajectory (e.g.
>>>> trajectories T1 + T2 + T3), then calculate projections along those
>>>> principal components separately (i.e. the projections for T1, T2, and
>>>> T3 along the combined PCs). The distributions for the individual
>>>> projections for PCs (particularly the low frequency ones) should
>>>> overlap pretty well, otherwise the trajectories are not converged -
>>>> note that overlap is a necessary but not sufficient condition of
>>>> convergence, ideally you will look at several different properties to
>>>> ascertain overall convergence. We used Kullback-Leibler divergence to
>>>> quantify the overlap of distributions, but that isn't the only way.
>>>> The SI in the given publication has some example scripts for CPPTRAJ
>>>>
>>>> Hope this helps,
>>>>
>>>> -Dan
>>>>
>>>> On Wed, Aug 5, 2015 at 2:24 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>>>> I’ve run 5 independent MD simulations of the same system. I’m seeking advice on how to compare the Principal Components derived from each trajectory to assess convergence of sampling.
>>>>>
>>>>>
>>>>> Regards
>>>>>
>>>>> George
>>>>> _______________________________________________
>>>>> 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)
>>>>
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>>>
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>>
>>
>>
>> --
>> -------------------------
>> 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/ <http://home.chpc.utah.edu/~cheatham/>
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
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```--
-------------------------
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 Thu Aug 06 2015 - 13:30:02 PDT
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