AMBER Archive (2009)

Subject: [AMBER] PCA analysis with ptraj

From: Alessandro Contini (alessandro.contini_at_unimi.it)
Date: Mon Nov 09 2009 - 11:00:19 CST

Dear Amber users,
I'm trying to perform essential dynamics on a amber trajectory using
ptraj. I succeded in generating requested eigenvectors and in projecting
them over trajectory. However, I didn't found a tool or a command to
allow the calculation of the contribution of each eigenvector to the
total motion of my system.

Another question regards the format of the covar matrix. The matrix is
3N X 3N, where N is the total number of atoms included in the analysis,
but is printed by ptraj as a set of values which do not correspond to
this scheme (i.e. I don't see 3N rows and 3N lines).

Thank you for your help

Alessandro Contini

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