AMBER Archive (2005)

Subject: AMBER: essential dynamics

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Wed Aug 24 2005 - 12:50:03 CDT


Hi Users:

I am trying to do an essential dynamics analysis of two simulation and I have
some question of the output that I get from g_anaeig and g_analyze. First
when I do the Overlap calculations between covariance analysis with g_anaeig
the -over option give me a plot with all the eigenvector and not the first 15
that I specified, How I use this plot? I need to go to the plot values and
find the overlap for the # eigenvectors that I decide to use. The other thing
is How I use the matrix from -inpr option? If the points go far from the
diagonal is not a good overlap???

With respect to g_analyze I have a question. What is the meaning of the plots
from the -dist and -ac options??? If someone could explain me or give some
references for background information it could help me to understand my
results.

Thank you in advance.

Best regards,
Anthony
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