[gmx-users] Temperature coupling

[Marcelo Vanean]

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."