You are simulating in vacuo! Otherwise the temperature gaps are way too large …
If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta <bharat.85.m...@gmail.com> wrote: > 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 <x.peri...@rug.nl> 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 <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 >> > > > > -- > -- > 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
