[gmx-users] non isotropic kinetic energy
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 7 19:09:37 CEST 2009
> we're running simulations of a water slab sandwiched by vacuum (ca. 2k
> waters, 3x3x12 nm^3 box) in NVT
> and look at the pressure tensor. We are surprised to find that the
> kinetic energy is equivalent (within statistical uncertainty) for x and
> y dim(parallel to the interface) but not in z dim. This appears to
> violate the equipartition theorem?
> This is gromacs 3.0 and 4.0 using berendsen thermostat.
First, try it with a real thermostat, second please report some numbers.
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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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