[gmx-users] Temperature coupling

[Marcelo Vanean]

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 <vanean22 at 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.
>