[AMBER] selecting frames with distribution

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Fri, 22 Jul 2016 15:02:45 +1000

Dear List,

I read a paper using aMD. It states "To analyze the resulting data,
principal component analysis (PCA) was performed on the Cα atom coordinates
of the N-intein in each frame. We then selected frames for which delta
V/kBT > 110"

How can I do post-processing to get the selected frames? The first step
requires that I carry out PCA analyses using cpptraj. It will print out
PC1, PC2. I am not sure what is delta V here? Potential energy or the free
energy resulting from 2D histogram of PC1 and PC2?


Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate
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Received on Thu Jul 21 2016 - 22:30:02 PDT
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