Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51
according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole <[email protected]> wrote: > > 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 <[email protected]> > 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 <[email protected]> > 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 <[email protected]> > >> 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 [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 > >> > > > > > > > > -- > > Bharat > > Ph.D. Candidate > > Biomolecular Engineering Laboratory > > Pusan National University > > South Korea > > Mobile no. - 010-5818-3680 > > -- > > 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 > -- -- 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
