[AMBER] Question about PCA tutorial

From: Abhilash J <md.scfbio.gmail.com>
Date: Wed, 29 Apr 2020 17:07:27 -0400


    I have a question on PCA. I did AMBER PCA tutorial and i have a
question. How to decide how many vectors to use. The PCA tutorial uses 3.
   ( runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat vecs 3 name
myEvecs nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-36&!.H= )

   While another Tutorial (on aMD "
https://ambermd.org/tutorials/advanced/tutorial22/section3.htm" ) uses 174
  ( analyze matrix matrixdat out evecs-ca.dat vecs 174 )

   I observe that 174 is also the same number of atoms the PCA used in
calculations per frame i.e. 174= 3*58. Where mask used is :1-58.CA,C,N)

   I also saw 2 papers referenced on this mailing list earlier in PCA from
Prof. Cheatham's lab they used 15 and 20 vectors (
https://pubs.acs.org/doi/abs/10.1021/jp4125099 and
https://pubs.acs.org/doi/abs/10.1021/ct400862k )
   Is there some general rule for this or some kind of pre PCA analysis is
required to best fit things. I am bit confused.


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Received on Wed Apr 29 2020 - 14:30:02 PDT
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