AMBER: post-processing replica exchange trajectory

From: Zhuang <>
Date: Wed, 29 Mar 2006 15:57:43 -0800

I have a question about post-processing replica exchange
trajectory...I have already done the simulaiton and I used the default
behavior which
writes mdcrd and mdinfo files in terms of a particular target
temperature rather than replica index...and such psedotrajectory does
not represent a physical path...I thought that was what I wanted...but
now some people suggest the reodering/permutation of sampled
configuration into this kind of pseudotrajectories will cause problems
in terms of correlation time and the estimation of statistical error
(John D. Chodera) I'm wondering if it's possible to postprocess
my pseudotrajectories back into true physcial there
any program out there that can automatically read in amber trajectory
and remlog file and spit out a new trajectory? thanks
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Received on Sun Apr 02 2006 - 06:10:12 PDT
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