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? 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? 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 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? I would appreciate any help. Thanks, Henri 1: Replica-Exchange Molecular Dynamics howto http://www.gromacs.org/Documentation/How-tos/REMD 2: Temperature generator for REMD-simulations http://folding.bmc.uu.se/remd/ 3: "md.log" file summary Replica exchange statistics Repl 2425 attempts, 1213 odd, 1212 even Repl average probabilities: Repl 0 1 2 3 4 5 6 7 8 9 10 ... Repl .55 .55 .55 .56 .56 .54 .56 .56 .56 .56 ... Repl number of exchanges: Repl 0 1 2 3 4 5 6 7 8 9 10 ... Repl 664 684 667 692 659 627 699 688 699 683 ... Repl average number of exchanges: Repl 0 1 2 3 4 5 6 7 8 9 10 ... Repl .55 .56 .55 .57 .54 .52 .58 .57 .58 .56 ... -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
