Dear David: Thank you for your answer. i still have several questions.
Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." After I finish the run, what option I should use for g_energy in order to get the viscosity? Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Yanmei Song wrote: >> >> Dear All: >> >> I wanted to get the viscosity of my simulated polymer system. From the >> manual it said that : GROMACS also has a non-equilibrium method for >> determining the viscosity" (page 123) Does this mean I just need to do >> a separate non-equilibrium MD run? In terms of mdp file, I just need >> to add the following options, right? >> acc_grps: >> accelerate: >> cos_acceleration: > > Just the last one. > >> >> My question is: first, how to set the value of cos_acceleration: ? > > You need to do a few values such that you can extrapolate to zero > acceleration. > >> Second, after I finish the run, how can I get the viscosity from the >> simulation result? Anyone has done this yet? Thank you so much for >> your answer in advance. >> > g_energy. > > J Chem Phys 116 (2002) 209-217 > J Chem Phys 119 (2003) 7308-7317 >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php