AMBER: problem with ptraj with calculating auto time correlation functions

From: Terry Lang <>
Date: Fri, 09 Mar 2007 10:36:14 -0800

Dear AMBER Community,

       I am trying to calculate some auto and cross time correlation
functions but have run into a snag. I am trying to use the following
script to compute both auto and cross time correlations:


ptraj prot.prm << EOF
trajin full_md_pres.crd
trajin run.crd
trajin run2.crd
trajin run3.crd
reference prot.crd
strip :WAT
strip .H
strip .Na+
rms reference
vector a1 :187 corr :233
vector a2 :188 corr :232
analyze timecorr vec1 a1 out a1.out
analyze timecorr vec1 a2 out a2.out
analyze timecorr vec1 a1 vec2 a2 out a1_a2.out

However, the only output I am getting is the a1_a2.out file. What am I
doing wrong?


P. Therese Lang
Post Doc
Alber Lab, UC Berkeley
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Received on Sun Mar 11 2007 - 06:07:31 PDT
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