The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp
Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > 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 > -- 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