Hi! I'm also working on REMD in these days. For temperature spacing you can use this web site: http://folding.bmc.uu.se/remd/ In order to find the most probable structure, which should be the global minimum, I think you can work with cluster analysis based on rmsd. Or it can be also useful a secondary structure analysis along the trajectory (if it is interesting for your system). If anyone else have some ideas I'm also looking for them.
Simone 2013/4/9 Nikunj Maheshwari <nixcrazyfor...@gmail.com> > Hi. Glad to know that your REMD was successful. We are trying to do the > same, but are stuck in between. > Can you tell us, how did you got the temperature spacing? > Thanks.... > > On Tue, Apr 9, 2013 at 11:59 AM, Shine A <shin...@iisertvm.ac.in> wrote: > > > Respected sir, > > > > I successfully completed REMD simulation. Now I am > > struggling with analysis part. Here how I select the global minimum from > > replica? Can you give some suggestions about the analysis part? > > -- > > 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
