AMBER Archive (2005)

Subject: Re: AMBER: question replica exchange acceptance ratio

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Jul 12 2005 - 18:43:01 CDT

Zhuang wrote:

>hi...Thank you so much for your reply...that's very helpful...just one
>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
>
>
>
yes, and this is the same as the 300K to 308K exchanges.
Each exchange is listed twice in the remlog, since each line
gives the original and new target T. So, you will find
300K 308K as well as 308K 300K.

>-------------------
>
>
>>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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>>
>>
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>>
>>
>>
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