[gmx-users] Temperature coupling

Mark Abraham mark.j.abraham at gmail.com
Sun Feb 23 22:52:44 CET 2014


Unfortunately, there is a fair bit of code in GROMACS that only the author
understands (if that many). Do have a look for any primary literature e.g.
cited from the manual. But you may need to identify and read the relevant
code fragment, unless you can devise a test of whether your understanding
of the algorithm inputs agrees with its output!

On Feb 23, 2014 8:42 PM, "Marcelo Vanean" <vanean22 at gmail.com> wrote:

> Still about the question of temperature coupling with method of the
> periodic perturbation I have the following question: Only the y and z
> components are rescaled in the temperature coupling?
> Original Post:
> "
> 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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