[gmx-users] Re: questions about Principal Component Analysis

[Tsjerk Wassenaar]

Hi Thomas,

Whether or not it makes sense to do PCA on the domain only depends on
the question you ask. It may well make sense if you aim at
characterizing the intra-domain motions. But be aware that you will
view those motions within the context of the rest of the protein. It
is quite likely that the internal motions depend on the interaction
with the surroundings.

Concerning the cosine content, there indeed seems to ba a transition.
But that is already evident from your RMSD plot. A lot of stuff is
still happening in the second half of the simulation. To see if the
last part of your simulation is in a (local) equilibrium, you can
calculate the average structure from that part, say the alst 10 or 20
ns, and determine the RMSD against the average. The RMSD should then
decrease towards the average and level off or oscillate around it to
assure you've reached some sort of equilibrium. On the basis of that
you could then decide whether it's worthwhile performing PCA on that
part only.

Cheers,

Tsjerk

On Sat, Mar 10, 2012 at 3:18 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> Regarding my second question, I have been experimenting with the cosine
> content using different portions of the trajectory and these are the results
> I got for the first principal component:
>
> proj-ev1_coscont_0-5ns.xvg 0.0174761
> proj-ev1_coscont_0-10ns.xvg 0.0283423
> proj-ev1_coscont_0-15ns.xvg 4.16906e-06
> proj-ev1_coscont_0-20ns.xvg 0.0689592
> proj-ev1_coscont_0-25ns.xvg 0.161691
> proj-ev1_coscont_0-30ns.xvg 0.298431
> proj-ev1_coscont_0-35ns.xvg 0.535732
> proj-ev1_coscont_0-40ns.xvg 0.767029
> proj-ev1_coscont_0-45ns.xvg 0.885829
> proj-ev1_coscont_0-50ns.xvg 0.906473
>
>
> proj-ev1_coscont_5-50ns.xvg  0.8823
> proj-ev1_coscont_10-50ns.xvg 0.751018
> proj-ev1_coscont_15-50ns.xvg 0.537473
> proj-ev1_coscont_20-50ns.xvg 0.357136
> proj-ev1_coscont_25-50ns.xvg 0.145889
> proj-ev1_coscont_30-50ns.xvg 0.0150995
> proj-ev1_coscont_35-50ns.xvg 0.00123905
> proj-ev1_coscont_40-50ns.xvg 0.00675679
> proj-ev1_coscont_45-50ns.xvg 0.0105643
>
>
> The total time I have run the simulation was 70ns, but judging from the
> steep increase of the RMSD (RMSD plot attached), I decided to exclude the
> first 20ns from the analysis. Hence the cosine content values above
> correspond to the last 50ns and the counting starts from the 20th ns.
>
> Clearly the convergence of the last 50ns is not good
> (proj-ev1_coscont_0-50ns.xvg: 0.906473), but the PC1 plot (attached) shows a
> steep decrease at ~30ns which looks like a conformational transition. It is
> also evident that the cosine content decreases drastically approximately at
> that point (25-50ns: 0.145889, 30-50ns.xvg: 0.0150995, 35-50ns.xvg:
> 0.00123905, etc.) and reached values that are not bad.
>
> Unfortunately, extending the simulation is not an option due to lack of time
> (I am forced to finish the manuscript soon). So would you recommend doing
> essential dynamics for the last 20ns?
>
> I would GREATLY appreciate any comments!!!
>
> Thomas
>
>
>
> On 7 March 2012 21:56, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>>
>>
>> Dear GROMACS community,
>>
>> I have two questions regarding PCA. I have run MD simulations for 70 ns
>> for a protein of 1100 amino acids, of which I decided - based on the RMSD -
>> to analyze the last 50.
>>
>> 1) The protein consists of 5 domains, out of which only one is of interest
>> in this study. Is it right to do draw conclusion from PCA restricted that
>> domain (400 aa)?
>>
>> 2) How can I find out if the simulation time is sufficient to do PCA?
>>
>> Thanks in advance for any feedback.
>>
>> Thomas
>>
>>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands