[gmx-users] Thermostatting in non-equilibrium dynamics

Ondrej Kroutil okroutil at gmail.com
Thu Mar 17 13:20:46 CET 2016

Dear all,

The question I have has been posted here by other user last year but with
not satisfactory answer (if I have searched properly!), so I'd like to open
this topic again.
It concerns non-equilibrium dynamics and thermostating. For simulations of
Poisseuille flow in explicit atomistic slabs we need to exclude certain
dimensions (direction of the applied external force, possibly also the
direction perpendicular to the slab) from calculation of kinetic energy for
thermostatting (absolutely important) as well as to turn on/off
thermostatting of rotational degrees of freedom (not so critical).

We see that some exclusion of the streaming velocities is implemented in
viscosity calculations, but we’d need to make it more general. In the same
way as one can specify pbc in xyz or xy, we’d love to be able to set
thermostatting of xyz velocities or xy only or x only. This is essential
for us to be able to use Gromacs for our non-equilibrium simulations.

We used the above thermostatting using our own code in publications:

M. Předota, P. T. Cummings, and D. J. Wesolowski: “Electric Double Layer at
the Rutile (110) Surface. 3. Inhomogeneous Viscosity and Diffusivity
Measurement by Computer Simulations” J. Phys. Chem. C
111, 3071 - 3079 (2007). http://dx.doi.org/10.1021/jp065165u

S. Pařez and M. Předota: “Determination of Distance-dependent Viscosity of
Mixtures in Parallel Slabs using Non-equilibrium Molecular Dynamics”, Phys.
Chem. Chem. Phys. 14, 3640-3650 (2012).

but now we work with larger flexible molecules and larger systems, which
are not suitable for our code.
Is such a request planned to be implemented in Gromacs?
If not, do you have hint in which source code file(s) we could modify this?
Thank you very much

    Ondřej Kroutil

Ondřej Kroutil
        ,,              Faculty of Science
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      OOO          The Czech Republic
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