Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help.
On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel <[email protected]> wrote: > Yanmei Song wrote: >> >> 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? > > At least equilibrium density. >> >> 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." > > You are interested (I assume) in the equilibrium viscosity, therefore you > need to do this extrapolation. You can not assume that a small acceleration > is small enough. >> >> After I finish the run, what option I should use for g_energy in order >> to get the viscosity? > > No option. > > Just do it (tm). >> >> Thank you so much in advance! >> >> On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel >> <[email protected]> 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. >>> [email protected] [email protected] http://folding.bmc.uu.se >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> > > > -- > 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. > [email protected] [email protected] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
