# Re: AMBER: question replica exchange acceptance ratio

From: Zhuang <ezhuang.chem.ucsb.edu>
Date: Tue, 12 Jul 2005 15:39:47 -0700

more question...if I type in

cat remlog | grep "308.00 300.00" | wc

this gives me how many exchange got accepted from 308K to 300K?

thanks

-------------------
> you'll need to process the remlog, right now that information
> isn't calculated for you. it is fairly easy to do, you can script it
> with grep/awk. one example would be
>
> cat remlog | grep "300.00 300.00" | wc
>
> that tells you how many exchanges for 300K did NOT
> get accepted. The acceptance ratio is (total-rejected)/total.
>
> for calculating ratio between a given pair of T1 and T2,
> keep in mind that you only attempt exchanges between each
> neighboring pair every other exchange attempt, since you exchange
> a given T up in temperature one step and down the next.
> So, for 10,000 overall exchange attempts, only 5,000 of
> them are for a given T1 and T2.
> In other words, for temperatures T1,T2,T3,T4 you
> attempt T1<->T2 one step, and T2<->T3 the next,
> then back to T1<->T2.
>
> so, you can cat remlog | grep "300.00 315.00" | wc but divide
> by total/2 to get the actual acceptance for that pair.
>
> We'll improve reporting of acceptances in the next Amber release.
>
>
> Zhuang wrote:
>
> >Hi...I'm trying to do replica exchange using amber8...and I don't
know
> >how to find out the acceptance ratio...I could't find the
information
> >in output file, log file or reminfo file...could anyone tell me how
to
> >find out what my acceptance ratios are...thank you very much
>
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Received on Tue Jul 12 2005 - 23:53:00 PDT
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