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