You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water …
It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the "Max drawing path length" in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta <[email protected]> wrote: > Dear Sir, > > I repeated the simulation again for 25 replicas with the following temp. > distribution . > > 280 > 289.1 > 298.5 > 308.2 > 318.2 > 328.6 > 339.3 > 350.3 > 361.7 > 373.5 > 385.6 > 398.1 > 411.1 > 424.4 > 438.3 > 452.5 > 467.2 > 482.4 > 498.1 > 514.3 > 531.0 > 548.3 > 566.1 > 584.5 > 603.5 > 623.2 > > 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 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 > Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 > .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 > > Repl number of exchanges: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 > Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 > 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 > > Repl average number of exchanges: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 > Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 > .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 > > The average acceptance ration is around 0.6 which is still high. > > The link for replica_temp,replica_index : > https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png > https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png > > The temp files look better but the index file looks weird ... > > Do i need to experiment with the gap difference in order to get the > required ration of 0.2-0.3 ?? There is some problem with the .mdp file > settings?? > > -- > Bharat > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
