Maybe. Either the model in the server is inapplicable for your system, or you've input data for the model incorrectly.
Mark On Thu, Apr 11, 2013 at 11:34 AM, Nikunj Maheshwari < nixcrazyfor...@gmail.com> wrote: > I understand the point now. Bigger the system, closer will be the spacing. > One thing though: The average energy (mu) returned by the web server for > each temperature is 7-8 times more than the actual energy returned after > REMD was over. > Is there something we are missing here? > > Thanks. > > On Tue, Apr 9, 2013 at 6:42 PM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > 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 > > > -- > 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
