[gmx-users] Temperature coupling

[Marcelo Vanean]

Michael Shirts, 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". The above sentences were transcribed exactly as they are in the
manual and the Hess article.

On Sat, Feb 22, 2014 at 9:46 PM, Marcelo Vanean <vanean22 at gmail.com> wrote:
> Vitaly V. Chaban, this is the question. How to remove the heat
> generated by viscous friction by heat bath without coupling the
> velocity profile to heat bath? Also, why to remove the velocity
> profile of the kinetic energy?
>
> On Sat, Feb 22, 2014 at 9:08 PM, Marcelo Vanean <vanean22 at gmail.com> wrote:
>> 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.
>>>
>>>