Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right!
I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta <bharat.85.m...@gmail.com> wrote: > Dear Sir, > > Thank you for your reply. I choose the temperature distribution using > t-remd calculator. Here's the link for index and temp files . > https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png > https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. > > > > > > > > On Sat, May 11, 2013 at 12:04 AM, XAvier Periole <x.peri...@rug.nl> wrote: > >> >> The replicas seem indeed to have exchange. Using a colour for the # >> replicas would help. >> >> I could not access to the first link. >> >> Note also that the increase of exchange ratio with the temperature suggest >> the distribution of the temperature is not optimal and may be with regular >> intervals? You want to use a exponential distribution. >> >> On May 10, 2013, at 4:53 PM, bharat gupta <bharat.85.m...@gmail.com> >> wrote: >> >>> 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 >> >> -- >> 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 >> > > > > -- > Bharat > Ph.D. Candidate > Biomolecular Engineering Laboratory > Pusan National University > South Korea > Mobile no. - 010-5818-3680 > -- > 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
