Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ...
I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0 1 2 3 4 5 6 7 8 9 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0 1 2 3 4 5 6 7 8 9 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0 1 2 3 4 5 6 7 8 9 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png<https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810>) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m<https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m&cid=1368069857486-810> ) -- Bharat -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists