[gmx-users] Temperature coupling

[Marcelo Vanean]

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.