[AMBER] Questions about dPCA.

From: Αυ±£Ρή <870726grin.163.com>
Date: Fri, 9 Jul 2021 12:29:47 +0800 (CST)

Dear Sir or Madam,
    I am writing to ask questions about how to analyze the results about dPCA (Dihedral covariance matrix calculation and projection for backbone phi/psi) analysis. I get the following instructions from AMBER Manuals, also I succeeded and got three .dat files. However, I don't know how to analyze it and don't know the detailed principle or theory, can you give me some advice or recommend some examples to me? Thank you very much. Looking forward to your reply.
32.13.2. Dihedral covariance matrix calculation and projection for backbone phi/psi (PCA)
parm ../1rrb_vac.prmtop
trajin ../1rrb_vac.mdcrd # Generation of phi/psi dihedral data
multidihedral BB phi psi resrange 2 run
# Calculate dihedral covariance matrix and obtain eigenvectors
matrix dihcovar dihedrals BB[*] out dihcovar.dat name DIH
diagmatrix DIH vecs 4 out modes.dihcovar.dat name DIHMODES
run # Project along eigenvectors
projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals BB[*] run

yours sincerely,
Baoyan Liu

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Received on Thu Jul 08 2021 - 22:00:02 PDT
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