[gmx-users] Temperature coupling

[Dr. Vitaly Chaban]

I think what is written means that the applied velocity is not
accounted for in the system kinetic properties, such as temperature,
during the simulation.


Dr. Vitaly V. Chaban


On Sat, Feb 22, 2014 at 11:16 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.
>>
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