I believe you are now posing the questions, where you are expected to open the source code yourself and read...
Dr. Vitaly V. Chaban On Sun, Feb 23, 2014 at 8:25 PM, Marcelo Vanean <vanea...@gmail.com> wrote: > 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. -- 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.
