AMBER Archive (2005)

Subject: Re: AMBER: question replica exchange acceptance ratio

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Tue Jul 12 2005 - 16:42:55 CDT

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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