I think what is written means that the applied velocity is not accounted for in the system kinetic properties, such as temperature, during the simulation.
Dr. Vitaly V. Chaban On Sat, Feb 22, 2014 at 11:16 PM, Marcelo Vanean <vanea...@gmail.com> wrote: > Dr. Vitaly Chaban, I know that g_energy is doing all the work for me. > However I want to understand the concepts. > > > On Fri, Feb 21, 2014 at 6:38 PM, Marcelo Vanean <vanea...@gmail.com> wrote: > >> I am trying to calculate the viscosity of water (spc model) by periodic >> perturbation method. The manual says (manual 4.6.5, pages 169 - 170): "To >> obtain the correct value for the viscosity the generated velocity profile >> should not be coupled to the heat bath, also the velocity profile should be >> excluded from the kinetic energy" and "The heat generated by the viscous >> friction is removed by coupling to a heat bath". I don't understand. How >> is possible to couple the system to the thermal bath, but not the >> velocity profile? >> >> Thank you in advance. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
