Hi Amber users,
I have 4 diffrent systems (monomer with and without ligand and
dimer with and whiout ligand).
I want to investigate and compare the cross correlation of
atomic fluctuation of these system.
for this purpose I should obtain the coorelation matrix from
matrix correl command of ptraj.
Is it possible that I construct a N X M matrix which N being the
number of atoms in one system (e.g. unliganded monomer) and M
being the number atom of another system (e.g. liganded
monomer).?or I have to construct correlation matrix for each
system. if this case is ture, Is it possible that have plot
which the right upper triangle consider one system, and the left
lower triangel consider another system?if yes how can I do it
with gnuplot or bio3d package?
also I have another question, As my simulation time is very long
I have the ".out" and "mdcrd" files (which have the information
of energy and ...) is very long that Excell ignor many data, how
could I reduce the number of frame?
Thank you very much for reply
Homa
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Received on Tue May 25 2010 - 20:00:03 PDT
