[gmx-users] non isotropic kinetic energy
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 15 13:00:22 CEST 2009
>> It is well known that water at a surface is ordered. How do you choose
>> the waters to analyze? If there is a net ordering in the system due to
>> external factors your system is not in equilibrium, but rather in a
>> steady state. However if you have e.g. vacuum-water-vacuum the
>> symmetry makes that equipartition should hold, provided the averaging
>> is over a time long enough such that water molecules sample both
>> Of course if you are worried about the constraints you could do a
>> simulation with flexible water for testing.
> "However if you have e.g. vacuum-water-vacuum the symmetry makes that
> equipartition should hold, provided the averaging is over a time long
> enough such that water molecules sample both surfaces."
I intended that *each* water molecule samples both surfaces...
> I agree 100%! We have averaged rotational and translation kinetic energy
> per water molecule for all water molecules in the system over the
> complete system (vacuum, water,vacuum) over a long time (so we think we
> are in equilibrum). So equipartition should hold, but it appears it
> doesn't (rot energy not equipartitioned).
> We have tryed with flexible water and here the problem vanishes (so
> equipartition works using the same analysis!). This difference between
> constraint and unconstraint water leads us to the concludion that there
> is aporblem with the constraints.
But if you can not reproduce this in bulk, you still haven't proven
anything because you are changing two things at the same time.
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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