[gmx-developers] Thermostatting in selected directions

Milan Predota predota at prf.jcu.cz
Thu Feb 2 14:49:31 CET 2017


thanks for a quick answer, but unfortunately the subtraction of 
streaming velocity is not applicable in my case.

I'm working on planar solid-liquid interfaces where the liquid flows 
along the surface under external electric field along the surface.

The streaming velocity profile is a complex function (from zero velocity 
at sticking surface to homogeneous in the bulk), unknown in advance and 
very dependent on the simulation conditions (surface charge, composition 
and type of ions, applied field).

I'm sure more people working on similar NEMD simulations, e.g. applying 
Poiseuille flow on liquid in a planar or cylindrical slab, must face 
this limitation.

I understand to tweak thermostats is not easy since they enter the 
integrator, but It is (at least in special cases) doable.

Simply I measure the kinetic energy only in selected directions, correct 
the number of degrees of freedom and scale/modify only selected 
directions, with the effect of thermostat on the others set to zero.

In my own Fortran MD code and the simulations I mention, I have checked 
that kinetic energy in the non-thermostated direction (as well as 
rotational energy - I was working with rigid SPC/E water) is very close 
to the ref_t.

It is a pity - otherwise Gromacs offers great support for the 
simulations I'm doing (e.g. semi-isotropic pressure coupling, external 
field/forces acting on selected groups, etc.).

I'd be happy to provide the physics if someone is able to modify the codes.



On 2/2/2017 2:20 PM, Berk Hess wrote:
> Hi,
> 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 Gromacs.
> Cheers,
> Berk
> 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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