Re: [gmx-users] REMD temperature spacing formula
Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- 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] REMD temperature spacing formula
Thanks for that link. I have used it, but it only takes system size properties. It doesn't take the potential energy values at all. I am looking if someone has used any alternate for temperature spacing generation? On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote: Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- 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] REMD temperature spacing formula
On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Thanks for that link. I have used it, but it only takes system size properties. It doesn't take the potential energy values at all. Actually it does, inasmuch as it uses parameters fitted to observed energy values, which you'd know from reading the abstract of the cited paper ;-). I am looking if someone has used any alternate for temperature spacing generation? Not sure what you're asking for. But you could try the REMD how-to guide in shameless plughttp://pubs.acs.org/doi/abs/10.1021/ct800016r/shameless plug, or the works of DA Kofke or UHE Hansmann will likely be instructive. Mark On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote: Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- 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 -- 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
