[gmx-users] essential dynamics

[Anthony Cruz]

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