RE: [gmx-users] equilibration of the simulated systems
That really depends on what property it is that you are interested in observing. You need to observe the dynamics of the property of interest, see over what time frames it changes, then ensure that you simulation time is enough to cover it equilibrating or changing. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Za Pour > Sent: Wednesday, 8 May 2013 4:58 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] equilibration of the simulated systems > > Dear gmx users > would you please tell me how I can be sure that my simulation time is > long > enough? is it appropriate way to use g_energy program and calculate > total energy ? > thank you > > -- > 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] equilibration of the simulated systems
yes. you can use g_energy to plot what you need (T, density or whatever) and decide if it is acceptable or not. In the latter case you simply have to extend your run (see http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) cheers Francesco On Tue, 7 May 2013, at 06:58 PM, Za Pour wrote: > Dear gmx users > would you please tell me how I can be sure that my simulation time is > long > enough? is it appropriate way to use g_energy program and calculate total > energy ? > thank you > > -- > 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 -- Francesco frac...@myopera.com -- 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] equilibration of the simulated systems
Dear gmx users would you please tell me how I can be sure that my simulation time is long enough? is it appropriate way to use g_energy program and calculate total energy ? thank you -- 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
