Re: [gmx-users] doubt in remd
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 listgmx-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 listgmx-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
Re: [gmx-users] doubt in remd
The gromacs web page links to this server for REMD temperature generation: http://folding.bmc.uu.se/remd/ On 9 Apr 2013, at 08:34, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] doubt in remd
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] doubt in remd
On Tue, Apr 9, 2013 at 8:29 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? Doing a simulation is useless until you have thought about what you want to observe from it. Only then can you design the simulation so it might show what you want to observe - or go do something more profitable if it won't be possible to observe! Constructing a free energy surface from the structures in a single ensemble is straightforward (e.g. Baumketner Shea papers), and that the simulation was REMD is immaterial. Mark -- gmx-users mailing listgmx-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 listgmx-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
