The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle).
In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta <bharat.85.m...@gmail.com> wrote: > Dear Sir, > > Here's the result for the REMD trial with large temperature gaps. > > Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 > 447.1 471.0 496.1 522.6 550.5 579.9 610.8 > > Out of md16.log : > > Replica exchange statistics > Repl 249 attempts, 125 odd, 124 even > Repl average probabilities: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 > Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 > .44 .46 > > Repl number of exchanges: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 > Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 > 57 58 > > Repl average number of exchanges: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 > Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 > .46 .46 > Average acceptance ratio : 0.46 > > But, the repli_index.xvg and replica_temp.xvg files still shows that the > replicas does not exchange equally well . > > https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png > https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png > > what could be wrong in this case?? Is it the mdp file settings or implicit > solvent setting. Does the time to replica to exhange also affects their > swapping ?? > > > > On Tue, May 14, 2013 at 12:24 AM, XAvier Periole <x.peri...@rug.nl> wrote: > >> >> 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 <bharat.85.m...@gmail.com> >> 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 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 >> >> -- >> 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 >> > -- > 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 -- 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
