[gmx-developers] Thermostatting in selected directions

Berk Hess hess at kth.se
Thu Feb 2 14:20:41 CET 2017


It is impossible to do this correct for the general case. If there are 
constraints present you can not assume the degrees of freedom (removed) 
are distributed equally over the dimensions. I have not though deeply 
about other issues, but I could image there are more.
It is much better to only subtract the single flow degree of freedom, as 
is done for e.g. the cosine acceleration profile that can be applied in 



On 2017-02-02 13:45, Milan Predota wrote:
> Hi,
> I need to do NEMD simulations of flows and for correct thermostatting 
> I'd need to select only 1 or 2 velocity directions used for setting 
> the temperature.
> I need  e.g. to calculate  kinetic energy only from v_x and v_y and 
> avoid v_z where there is a nonzero and a priory unknown streaming 
> velocity.
> The temperature coupling would act of course only on the v_x and v_y 
> components, leaving the v_z to equilibrate due to intermolecular 
> interactions.
> I have done this in my own MD code (only water + ions) with success, 
> http://dx.doi.org/10.1021/acs.langmuir.6b02493
> but I'm now using Gromacs for more complex molecules.
> I don't find this feature even in Gromacs 2016. *Is there a plan to 
> incorporate this feature in Gromacs?*
> I guess to modify the source code by myself would be a tedious and 
> dangerous task.
> I have found out that LAMMPS probably has this feature
> http://lammps.sandia.gov/doc/compute_modify.html
> http://lammps.sandia.gov/doc/fix_temp_berendsen.html 
> <http://lammps.sandia.gov/doc/fix_temp_csvr.html>
> http://lammps.sandia.gov/doc/fix_temp_csvr.html
> http://lammps.sandia.gov/doc/fix_nh.html
> but I'd prefer to continue using Gromacs.
> Many thanks,
> Milan
> Institute of Physics and Biophysics
> Faculty of Science, University of South Bohemia
> Branisovska 1760, 370 05 Ceske Budejovice
> Czech Republic

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