Re: [AMBER] aMD plot

From: ʢ <>
Date: Sun, 4 Jan 2015 07:22:55 +0800 (GMT+08:00)

 projections of trajectory on PC1 and PC2 :

    cpptraj> projection modes evecs-ca.dat out pca12-ca beg 1 end 3 .CA

     The resulting file have three column: Mode1 mode2 mode3

reweighting :

     python -input Phi_Psi -Emax 100 -discX 6 -discY 6 -job amdweight_MC -order 10 -weight weights.dat

But in the section3 of A22 tutorial there isn't Phi_Psi-related file generated during the PC1-2 projection. For the PCA plot, what is the alternative Phi_Psi-like file?

The most important is where is the third dimemsion from? From the one column of reweghting generated file: KDE-reweight.dat.

And cut two columns of pca12-ca and one column of KDE-reweight.dat to form a new three column of another file to plot the final figure:

PC1(Angstrom)-PC2(Angstrom)-Energy(kCal/mol) => 3D plot

Is that true? The tutorial doesn't tell these details.


Message: 6
Date: Sat, 3 Jan 2015 12:38:31 +0200
From: Thomas Evangelidis <>
Subject: Re: [AMBER] aMD plot
To: AMBER Mailing List <>
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He needs to reweight first since he did accelerated MD.

Once you have the projections of your trajectory on PC1 and PC2 use script to reweight and make the histogram:
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Received on Sat Jan 03 2015 - 15:30:03 PST
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