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 Sun May 23 2010 - 20:00:03 PDT
