[gmx-users] Temperature coupling

[Michael Shirts]

See the following for more information:

"Effects of Temperature Control Algorithms on Transport Properties and
Kinetics in Molecular Dynamics Simulations"

http://pubs.acs.org/doi/abs/10.1021/ct400109a

When discussing velocity profile, I believe this is referring to any
external driving force that results in net movement of the system.

On Sat, Feb 22, 2014 at 4:21 PM, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
> I do not know what the manual says, but if you are talking about
> viscosity computation through cos-like acceleration, then g_energy is
> doing all the work for you.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Fri, Feb 21, 2014 at 10:38 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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