AMBER Archive (2007)

Subject: Re: AMBER: problem with ptraj with calculating auto time correlation functions

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 09 2007 - 19:01:44 CST

On Fri, Mar 09, 2007, Terry Lang wrote:
>
> 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:
>
> #!/bin/csh
>
> 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

You need to specify both "vec1" and "vec2", even if they are the same, e.g.:

analyze timecorr vec1 a1 vec2 a1 out a1.out
analyze timecorr vec1 c2 vec2 a2 out a2.out

[The Amber 8 manual had an error here, but the Amber 9 manual has it specified
correctly.]

...hope this helps...dac

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