RE: [gmx-users] REMD question
Michael, Thank you for your answer. On the other hand, I´m not implementing, I´m using REMD.. I miss wrote it. Nathalia -Mensaje original- De: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] En nombre de Michael Shirts Enviado el: lunes, 28 de mayo de 2012 08:09 p.m. Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] REMD question Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibration at constant pressure. On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces wrote: > Dear Gromacs Users, > > > > We are implementing REMD method in Gromacs in protein folding, in your > web page you give some steps that don´t mention any step about NPT > stabilization. This step is necessary to run REMD simulations? > > > > Thank you in advance, > > > > Nathalia > > > > > -- > 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 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 question
Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibration at constant pressure. On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces wrote: > Dear Gromacs Users, > > > > We are implementing REMD method in Gromacs in protein folding, in your web > page you give some steps that don´t mention any step about NPT > stabilization. This step is necessary to run REMD simulations? > > > > Thank you in advance, > > > > Nathalia > > > > > -- > 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 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 question
Joohyun Kim wrote: Dear All, How trajectories are generated with REMD option? I have 16 replicas and am having 16 trajectories. In each trajectory, temperature is same? Then, how can I look at the temperature variation according to exchanges? you will have to write a script to do that based on the output in the md0.log file. Joohyun ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
