[gmx-users] non isotropic kinetic energy

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 7 19:09:37 CEST 2009

aherz wrote:
> Hi,
> 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.

> Alex
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list