Still about the question of temperature coupling with method of the periodic perturbation I have the following question: Only the y and z components are rescaled in the temperature coupling?
Original Post: " 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.