On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari <nixcrazyfor...@gmail.com> wrote: > Thats true with our case as well. The spacing was very small, and we got > almost 70 replicas for our protein between 280-410K. > That's why, we are thinking of any alternate way of getting the spacing, > and started using polynomial fit of the average energies we obtained from > our first run. Do you have any thoughts on that?
You can space them however you want, but you will only get exchanges if they are close enough in temperature. The spacing returned by the generator is not small because it wants you to use excess compute resources! It needs to be small for big systems. Mark > On Tue, Apr 9, 2013 at 2:03 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > >> I used the REMD temperature generator. Needless to say, we got really >> tight spacing and the enhancement to the sampling was probably small. The >> whole setup was pretty experimental. The run was completed. >> >> Erik >> >> On 9 Apr 2013, at 10:01, Nikunj Maheshwari <nixcrazyfor...@gmail.com> >> wrote: >> >> > How did you get the final temperature spacing for the run? Did you get >> the >> > fitted values using polynomial fit? >> > Was the run completed? >> > >> > On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund <er...@xray.bmc.uu.se> >> wrote: >> > >> >> I've tried one with 666 aa, but with no publishable results. >> >> >> >> On 9 Apr 2013, at 09:47, Nikunj Maheshwari <nixcrazyfor...@gmail.com> >> >> wrote: >> >> >> >>> Dear all... >> >>> >> >>> Does anyone has any idea what is the maximum protein size for which a >> >>> successful REMD run has taken place? >> >>> We have went through lots of research papers, but could not find any >> >>> protein/peptide above 100 aa related to REMD. >> >>> We have a protein of 292 aa. >> >>> >> >>> Thanks. >> >>> -- >> >>> 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 -- 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
