[gmx-users] frozen group in pressure coupling
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 3 22:02:01 CET 2004
On Wed, 3 Mar 2004, qiao rui wrote:
> I am wondering if anyone could give me some hints on the following
> 1. In pressure coupling, does one update the position of the
>frozen group? The manual says that the coordinate of every atom will be
>scaled, but from the simulation results, it seems that the frozen group is
>not scaled. Am I making some mistakes here?
No, these positions are not scaled.
> 2. I couple the xx-direction pressure to one bar, and getting the
>huge numbers of pressure in other directions, is this OK?
Are these pressures negative? It is very likely that we do include the
interactions with frozen atoms in the virial, while they have zero
kinetic energy. In this case the pressure is incorrect. If you are somehow
certain that your density os correct you can run NVT for a while,
determine averages pressures, and if you need to run NPT, couple to these
>Beckman Institute, UIUC
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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