AMBER Archive (2007)

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

From: Terry Lang (terry_at_lego.berkeley.edu)
Date: Sat Mar 10 2007 - 09:59:09 CST

Dear Dave,

       Thanks for the fix! It is working now. Just FYI, though, I was
using the AMBER 9 manual to create the file. The typo is still there on
pages 261-262.

Terry

David A. Case wrote:
> 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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-- 
P. Therese Lang
Post Doc
Alber Lab, UC Berkeley

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