Dear Daniel,
I am attaching pca1 vs pca2 gnuplot. Can you please suggest me what
these orange and purple color code represent to my result.
On Tue, Nov 28, 2017 at 2:10 PM, Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> Dear,
> I got the result for PCA.
>
> As I am new to this, I could not able to analyze the result.
> Can you help me. I am attaching my plot.
>
>
> On Mon, Nov 27, 2017 at 5:50 PM, Nisha Amarnath Jonniya <
> phd1601271002.iiti.ac.in> wrote:
>
>> Thanks Elvis for the reply.
>> Will do and let you know.
>>
>> On Mon, Nov 27, 2017 at 5:35 PM, Elvis Martis <elvis.martis.bcp.edu.in>
>> wrote:
>>
>>> Hi,
>>> Still not clear what is wrong.
>>> I am attaching a script for PCA. Just copy it in the correct directory
>>> and run "cpptraj -i pca.in" <without quotes.>
>>> Just tell me if you get the same error.
>>>
>>> Best Regards
>>> Elvis Martis
>>> Mumbai, INDIA.
>>>
>>> ________________________________________
>>> From: Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in>
>>> Sent: 27 November 2017 14:15
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] PCA eigenvalues
>>>
>>> Dear Elvis
>>>
>>> Though I tried with your comment, but still I got the following error
>>> after execution of hist command .
>>> Is it the error with parm.top file??
>>>
>>>
>>> can you help me.
>>>
>>>
>>>
>>>
>>> ANALYSIS: Performing 3 analyses:
>>> 0: [hist ex:1 bins 100 out ex_hist.gnu norm name ex_1]
>>> Error: HistBin: Max (-16.4714) must be greater than min (-16.4714)
>>> Error: Could not set up histogram dimension 'ex:1'
>>> Error: In Analysis [hist]
>>> 1: [hist ex:2 bins 100 out ex_hist.gnu norm name ex_2]
>>> Error: HistBin: Max (17.4431) must be greater than min (17.4431)
>>> Error: Could not set up histogram dimension 'ex:2'
>>> Error: In Analysis [hist]
>>> 2: [hist ex:3 bins 100 out ex_hist.gnu norm name ex_3]
>>> Error: HistBin: Max (-21.5487) must be greater than min (-21.5487)
>>> Error: Could not set up histogram dimension 'ex:3'
>>> Error: In Analysis [hist]
>>>
>>> TIME: Analyses took 0.0161 seconds.
>>>
>>> RUN TIMING:
>>> TIME: Init : 0.0545 s ( 0.00%)
>>> TIME: Trajectory Process : 2025.7628 s (100.00%)
>>> TIME: Action Post : 0.0000 s ( 0.00%)
>>> TIME: Analysis : 0.0161 s ( 0.00%)
>>> TIME: Data File Write : 0.0000 s ( 0.00%)
>>> TIME: Other : 0.0142 s ( 0.00%)
>>> TIME: Run Total 2025.8477 s
>>> ---------- RUN END ---------------------------------------------------
>>> [readdata evececs name Evecs]
>>> Reading 'evececs' as Evecs file with name 'Evecs'
>>> Reading modes from evececs
>>> Warning: DataSet 'Evecs' already present.
>>> Error: reading datafile evececs
>>> Error: Could not read data file 'evececs'.
>>> 1 errors encountered reading input.
>>> Warning: Set 'ex_1' contains no data.
>>> Warning: Set 'ex_2' contains no data.
>>> Warning: Set 'ex_3' contains no data.
>>> Warning: File 'ex_hist.gnu' has no sets containing data.
>>> TIME: Total execution time: 8669.3131 seconds.
>>> Error: Error(s) occurred during execution.
>>>
>>>
>>>
>>>
>>>
>>> On Fri, Nov 24, 2017 at 5:45 PM, Elvis Martis <elvis.martis.bcp.edu.in>
>>> wrote:
>>>
>>> > Hi,
>>> > Here is the problem
>>> > "runanalysis diagmatrix ex_covar out evececs 20 name
>>> exEvecs:1-273&!.H="
>>> > Seems like you missed a space there.
>>> > Try to replace that line with this
>>> > "runanalysis diagmatrix ex_covar out evececs 20 name ex Evecs
>>> :1-273&!.H="
>>> >
>>> >
>>> > Best Regards
>>> > Elvis Martis
>>> > Mumbai, INDIA.
>>> >
>>> > ________________________________________
>>> > From: Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in>
>>> > Sent: 24 November 2017 17:09
>>> > To: AMBER Mailing List
>>> > Subject: Re: [AMBER] PCA eigenvalues
>>> >
>>> > Dear all,
>>> >
>>> > As I was also doing PCA analysis. This mail helped me too but I
>>> got
>>> > error in execution of hist: command .
>>> >
>>> > These are my script.
>>> >
>>> > parm complex_solv.prmtop
>>> > trajin trajout10-51.mdcrd
>>> > rms first :1-273&!.H=
>>> > average crdset ex_average
>>> > createcrd ex_trajectories
>>> > run
>>> > crdaction ex_trajectories rms ref ex_average :1-273&!.H=
>>> > crdaction ex_trajectories matrix covar name ex_covar :1-273&!.H=
>>> > runanalysis diagmatrix ex_covar out evececs 20 name exEvecs:1-273&!.H=
>>> > readdata evececs name Evecs
>>> > runanalysis modes eigenval name Evecs out evalfrac.dat
>>> >
>>> > crdaction ex_trajectories projection ex modes Evecs beg 1 end 3
>>> > :1-273&!.H= crdframes 84000
>>> >
>>> > hist ex:1 bins 100 out 5drb_hist.gnu norm name ex_1
>>> > hist ex:2 bins 100 out 5drb_hist.gnu norm name ex_2
>>> > hist ex:3 bins 100 out 5drb_hist.gnu norm name ex_3
>>> > run
>>> > readdata evececs name Evecs
>>> > parm complex_solv.prmtop
>>> > parmstrip !(:1-273&!.H=)
>>> > parmwrite out ex_modes.prmtop
>>> > runanalysis modes name Evecs trajout ex_mode1.nc pcmin -100 pcmax 100
>>> > tmode
>>> > 1 trajoutmask :1-273&!.H= trajoutfmt netcdf
>>> > runanalysis modes name Evecs trajout ex_mode2.nc pcmin -100 pcmax 100
>>> > tmode
>>> > 2 trajoutmask :1-273&!.H= trajoutfmt netcdf
>>> > runanalysis modes name Evecs trajout ex_mode3.nc pcmin -100 pcmax 100
>>> > tmode
>>> > 3 trajoutmask :1-273&!.H= trajoutfmt netcdf
>>> >
>>> >
>>> >
>>> > I am getting error in hist command with following error
>>> >
>>> >
>>> > Data set 'ex:1' not found.
>>> > Error: Dataset ex:1 not found.
>>> > Error: Could not setup analysis [hist]
>>> > 1 errors encountered reading input.
>>> > Warning: File 'ex_hist.gnu' has no sets containing data.
>>> >
>>> >
>>> >
>>> >
>>> > Can you please guide me further how to rectify this problem.
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Fri, Nov 24, 2017 at 12:26 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za
>>> >
>>> > wrote:
>>> >
>>> > > Hi Dan,
>>> > >
>>> > > Thanks so much for the great advice you sent earlier.
>>> > > It worked out well but I noticed the following warning in the output:
>>> > > Warning: Frame 25 Coordinates out of bounds (100). What does it mean
>>> and
>>> > > should I be worried about it?
>>> > >
>>> > > The projection of PC1 vs PC2 was written as a gnu file like you
>>> suggested
>>> > > and displays a scatter of frames. However, the plot has a black
>>> > background
>>> > > and purple dots for each frame which is really not very clear.
>>> > > Is there any way that I can change the colour or write it in another
>>> > > format? I can't seem to edit the plot at all in gnuplot.
>>> > >
>>> > > Regards
>>> > >
>>> > > Lizelle
>>> > >
>>> > > ________________________________________
>>> > > From: Daniel Roe <daniel.r.roe.gmail.com>
>>> > > Sent: 20 November 2017 05:53:21 PM
>>> > > To: AMBER Mailing List
>>> > > Subject: Re: [AMBER] PCA eigenvalues
>>> > >
>>> > > s.dat vHi,
>>> > >
>>> > > On Sat, Nov 18, 2017 at 10:05 AM, Lizelle Lubbe <
>>> LBBLIZ002.myuct.ac.za>
>>> > > wrote:
>>> > > > Hi Amber users,
>>> > > >
>>> > > > I have performed PCA analysis on my MD trajectories in cpptraj and
>>> > would
>>> > > like to plot the fraction of total variance vs eigenvalue as shown in
>>> > > figure s9 of Roe et al 2014 (j phys chem b, 118, 3543-3552).
>>> > >
>>> > > To do this you'll want to calculate all principal components (i.e.
>>> > > eigenvectors) from your covariance matrix, so 3 * the number of
>>> > > selected atoms. Then you run the 'modes' analysis command with the
>>> > > 'eigenval' keyword on the resulting modes data, e.g.
>>> > >
>>> > > runanalysis diagmatrix myCovar out evececs 246 name myEvecs :1-4&!.H=
>>> > > runanalysis modes eigenval name myEvecs out evalfrac.dat
>>> > >
>>> > > > I also want to have a scatter plot of pc1 vs pc2 and pc2 vs pc3 to
>>> > > visualize clusters in this space.
>>> > > > Could someone please guide me in how this can be accomplished?
>>> > >
>>> > > For these, just give desired the principal component projection data
>>> > > set names to the 'hist' command, e.g. for the projection of PC 1 vs
>>> 2:
>>> > >
>>> > > hist Ndom:1 Ndom:2 bins 100 out Ndom_hist.gnu norm name Ndom_1_2
>>> > >
>>> > > > Also, how should the pca histogram analysis be interpreted?
>>> > >
>>> > > This is a lot trickier. As you probably know principal components
>>> > > represent axes that in this case describe variance in the selected
>>> > > atoms in your system. So PCs can tell you about what the dominant
>>> > > modes of motion in your system look like, but generally may not tell
>>> > > you how your system actually moves. Personally I like to visualize
>>> the
>>> > > modes of motion with the 'trajout' keyword of 'modes' (which it
>>> > > appears you are doing). It can also help to look at the so-called
>>> > > 'porcupine plots' - I use the nmwiz plugin for VMD (it appears you
>>> are
>>> > > doing that as well).
>>> > >
>>> > > Hope this helps,
>>> > >
>>> > > -Dan
>>> > >
>>> > > >
>>> > > > This is my pca script:
>>> > > >
>>> > > > trajin traj.nc
>>> > > >
>>> > > > rms first :1-720&!.H=
>>> > > >
>>> > > > average crdset Ndom_average
>>> > > >
>>> > > > createcrd Ndom_trajectories
>>> > > >
>>> > > > run
>>> > > >
>>> > > > crdaction Ndom_trajectories rms ref Ndom_average :1-720&!.H=
>>> > > >
>>> > > > crdaction Ndom_trajectories matrix covar name Ndom_covar
>>> :1-720&!.H=
>>> > > >
>>> > > > runanalysis diagmatrix Ndom_covar out Ndom_evecs.dat vecs 20 name
>>> > > NdomEvecs nmwiz nmwizvecs 3 nmwizfile Ndom_pca.nmd nmwizmask
>>> :1-720&!.H=
>>> > > >
>>> > > > crdaction Ndom_trajectories projection Ndom modes NdomEvecs beg 1
>>> end 3
>>> > > :1-720&!.H= crdframes 1,3000
>>> > > >
>>> > > > hist Ndom:1 bins 100 out Ndom_hist.agr norm name Ndom_1
>>> > > >
>>> > > > hist Ndom:2 bins 100 out Ndom_hist.agr norm name Ndom_2
>>> > > >
>>> > > > hist Ndom:3 bins 100 out Ndom_hist.agr norm name Ndom_3
>>> > > >
>>> > > > run
>>> > > >
>>> > > > clear all
>>> > > >
>>> > > > readdata Ndom_evecs.dat name Evecs
>>> > > >
>>> > > > parm NDOM_CPLX_rnb_stripped_box.prmtop
>>> > > >
>>> > > > parmstrip !(:1-720&!.H=)
>>> > > >
>>> > > > parmwrite out Ndom_modes.prmtop
>>> > > >
>>> > > > runanalysis modes name Evecs trajout Ndom_mode1.nc pcmin -100
>>> pcmax 100
>>> > > tmode 1 trajoutmask :1-720&!.H= trajoutfmt netcdf
>>> > > >
>>> > > > runanalysis modes name Evecs trajout Ndom_mode2.nc pcmin -100
>>> pcmax 100
>>> > > tmode 2 trajoutmask :1-720&!.H= trajoutfmt netcdf
>>> > > >
>>> > > > runanalysis modes name Evecs trajout Ndom_mode3.nc pcmin -100
>>> pcmax 100
>>> > > tmode 3 trajoutmask :1-720&!.H= trajoutfmt netcdf
>>> > > >
>>> > > > Kind regards
>>> > > >
>>> > > > Lizelle Lubbe
>>> > > > PhD Chemical Biology candidate
>>> > > > University of Cape Town
>>> > > > Disclaimer - University of Cape Town This e-mail is subject to UCT
>>> > > policies and e-mail disclaimer published on our website at
>>> > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
>>> from
>>> > > +27 21 650 9111. If this e-mail is not related to the business of
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>>> > > is sent by the sender in an individual capacity. Please report
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>>> > > incidents or abuse via csirt.uct.ac.za
>>> > > > _______________________________________________
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>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > -------------------------
>>> > > Daniel R. Roe
>>> > > Laboratory of Computational Biology
>>> > > National Institutes of Health, NHLBI
>>> > > 5635 Fishers Ln, Rm T900
>>> > > Rockville MD, 20852
>>> > > https://www.lobos.nih.gov/lcb
>>> > >
>>> > > _______________________________________________
>>> > > AMBER mailing list
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>>> > > Disclaimer - University of Cape Town This e-mail is subject to UCT
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>>> > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
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>>> > > is sent by the sender in an individual capacity. Please report
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>>> > >
>>> >
>>> >
>>> >
>>> > --
>>> >
>>> > Nisha Amarnath Jonniya
>>> > PhD Research Scholar
>>> > Biosciences and Biomedical Engineering
>>> > Indian Institute of Technology, Indore
>>> > India
>>> > _______________________________________________
>>> > AMBER mailing list
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>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
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>>> >
>>>
>>>
>>>
>>> --
>>>
>>> Nisha Amarnath Jonniya
>>> PhD Research Scholar
>>> Biosciences and Biomedical Engineering
>>> Indian Institute of Technology, Indore
>>> India
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>> --
>>
>> Nisha Amarnath Jonniya
>> PhD Research Scholar
>> Biosciences and Biomedical Engineering
>> Indian Institute of Technology, Indore
>> India
>>
>>
>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
>
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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- application/postscript attachment: pca.eps
Received on Wed Nov 29 2017 - 03:30:02 PST
