----- Original Message ----- From: henri mone <[email protected]> Date: Saturday, August 21, 2010 23:06 Subject: [gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation To: [email protected]
> Calculate observed "Acceptance Ratio" from REMD simulation > > Dear Gromacs users, > > I used the Gromacs how-to [1] to setup a REMD simulation. The targeted > acceptance ratio was P_acp=15%, I used the temperature generator > web-service [2] 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 > correct? 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 [3]. 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 [1]. 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. Mark
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