AMBER Archive (2004)

Subject: AMBER: about correlation calculation in ptraj

From: jz7_at_duke.edu
Date: Tue Jul 27 2004 - 16:20:53 CDT

Dear all,

Has anyone used ptraj to do the correlation calculation and essential
dynamics analysis? What is the normal time-scale for this kind of
calculation in ptraj? For my case, I have about 300 atoms included
(900x900 matrix) and a trajectory of 500 frames. How long would the
calculation take (command like "matrix covar name mcovar" and "analyze
matrix mcovar out evec.pev vecs 25")? I have been running calculation for
about two hours, but still nothing output (ptraj stops at "Analyzing
accumulated data").

Thanks a lot!

Best,
Jeny
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