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<div class="moz-cite-prefix">Hi,<br>
<br>
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.<br>
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.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2017-02-02 13:45, Milan Predota wrote:<br>
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cite="mid:330c0320-cdc1-9af6-fa3d-acd3a257394e@prf.jcu.cz"
type="cite">
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<p>Hi,</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>I have done this in my own MD code (only water + ions) with
success, <a moz-do-not-send="true"
href="http://dx.doi.org/10.1021/acs.langmuir.6b02493">http://dx.doi.org/10.1021/acs.langmuir.6b02493</a></p>
<p>but I'm now using Gromacs for more complex molecules.</p>
<p>I don't find this feature even in Gromacs 2016. <b>Is there a
plan to incorporate this feature in Gromacs?</b></p>
<p>I guess to modify the source code by myself would be a tedious
and dangerous task.<br>
</p>
I have found out that LAMMPS probably has this feature<br>
<a moz-do-not-send="true"
href="http://lammps.sandia.gov/doc/compute_modify.html">http://lammps.sandia.gov/doc/compute_modify.html</a><br>
<a moz-do-not-send="true"
href="http://lammps.sandia.gov/doc/fix_temp_csvr.html">http://lammps.sandia.gov/doc/fix_temp_berendsen.html</a><br>
<a moz-do-not-send="true"
href="http://lammps.sandia.gov/doc/fix_temp_csvr.html">http://lammps.sandia.gov/doc/fix_temp_csvr.html</a><br>
<a moz-do-not-send="true"
href="http://lammps.sandia.gov/doc/fix_nh.html">http://lammps.sandia.gov/doc/fix_nh.html</a><br>
<br>
but I'd prefer to continue using Gromacs.<br>
Many thanks,<br>
Milan<br>
<br>
Institute of Physics and Biophysics<br>
Faculty of Science, University of South Bohemia<br>
Branisovska 1760, 370 05 Ceske Budejovice<br>
Czech Republic <br>
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