Thank you Daniel,
It worked. I have a couple of queries.
1. In my script
kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name PC1-PC2-1
kde T1:2 kldiv T2:2 klout KL-PC.agr bins 400 name PC1-PC2-2
kde T1:3 kldiv T2:3 klout KL-PC.agr bins 400 name PC1-PC2-3
kde T1:4 kldiv T2:4 klout KL-PC.agr bins 400 name PC1-PC2-4
kde T1:5 kldiv T2:5 klout KL-PC.agr bins 400 name PC1-PC2-5
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?
2. In the affirmative, I guess I should do the same for run 1 and 3, 1 and 4, etc. Am I right?
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?
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
>>> you should be able to adapt for your use.
>>>
>>> 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.
>>>>
>>>> Thank in advance for any guidance and advice
>>>>
>>>> Regards
>>>>
>>>> George
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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)
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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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Received on Thu Aug 06 2015 - 07:30:03 PDT
