[gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation
mark.abraham at anu.edu.au
Sat Aug 21 15:40:58 CEST 2010
----- Original Message -----
From: henri mone <henrimone at gmail.com>
Date: Saturday, August 21, 2010 23:06
Subject: [gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation
To: gmx-users at gromacs.org
> Calculate observed "Acceptance Ratio" from REMD simulation
> Dear Gromacs users,
> I used the Gromacs how-to  to setup a REMD simulation. The targeted
> acceptance ratio was P_acp=15%, I used the temperature generator
> web-service  to get the temperature spacing. From the test
> simulation I want to calculate the observed acceptance ratio P_obs.
> The last md.log file gives a "Replica exchange statistic". I got
> following questions regarding on how to calculate P_obs.
> 1. To get P_obs from simulation I have to calculate the ratio between
> the successful exchange and total exchange attempts.
> Is this correct? I checked several papers and books (Frenkel/Smit,
> etc.), I only found the formula how to calculate the temperature
> spacing given P_acp. But I couldn't find a formula or definition how
> to calculate P_obs from a simulation. Is the above definition of P_obs
Yep. It's about the easiest thing you'll ever calculate from an MD simulation.
> 2. The md.log file "Replica exchange statistic" gives in my case
> following summary . For temperature T0 to T1 there wehre 664
> successful exchanges. The number of exchange attempts were 1213. The
> ratio 664/1213 gives 55%. Would the P_obs=55% , is this correct?
> 3. A observed ratio of P_obs=50% given a targeted acceptance
> ratio of
> P_acp=15% is quite high.
> What can be the reason for this large discrepancy?
Probably, you've not done what you've think you've done with the web server.
> 4. Could the Gromacs users, admin etc. please add some more
> information to the REMD Howto . In particular regarding how to
> calculate P_obs?
It's probably not there because it's regarded as straightforward :-)
> It would be a really useful for the Gromacs users.
> Can I as a Gromacs user add some more information to the howto
> or do I
> need a login?
The wiki-style web pages are largely a community effort. As such, contributions are welcome, subject to the usual wiki considerations that you might get edited mercilessly, etc. You'll need a login, and that might require someone to approve you, but that would normally be forthcoming.
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