[gmx-users] Temperature coupling

Michael Shirts mrshirts at gmail.com
Sun Feb 23 02:59:51 CET 2014

I'm pretty sure that viscous friction is not what is referred to when
it's talking about a velocity profile; it's the COM velocities.

On Sat, Feb 22, 2014 at 7:46 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.
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