[gmx-users] Temperature coupling

[Marcelo Vanean]

Michael Shirts, in this article is not discussed about the periodic
perturbation method to calculate viscosity. Anyway, thank you.

On Sat, Feb 22, 2014 at 7:16 PM, Marcelo Vanean <vanean22 at gmail.com> wrote:
> 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.
>
>