[gmx-users] parinello-rahman coupling

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 27 13:52:38 CEST 2007

Hi Loris,

Enjoying the nice weather here, I'll just give a gentle reiteration of
previous remarks. What you observe is caused by the fact that you only
have a very small system from which you try to extract a macroscopic
property (i.e. defined only for large systems). The large fluctuations
are normal. It would be a good idea to read some general texts about
statistical mechanics and molecular dynamics and before posting a
question to the user list, it would also be good to browse through the
archives of this list, to see if the question you're about to ask has
already been answered (and trust me, this one has been, many times).

Good luck with your simulations,


On 3/27/07, lorix <Loris.Moretti at pharm.unige.ch> wrote:
> Dear gmx-users,
> I am a new one...
> coming to the point...I am simulating in parallel different
> configurations and settings of a protein
> around 300 residues large plus approximately 12000 water molecules.
> I am simulating NPT with berendsen for P and T to equilibrate over 100
> ps and then the simulation
> for several ns (5-20) with nose-hoover for T and parinello-rahman for P.
> But in the last step I cannot find a value for tau_p to maintained and
> average of 1 bar.
> Reducing the tau_p value (0.06, 0.05 and 0.01) I get many messages in
> the log file like:
> Grid: 11 x 10 x 9 cells
> Grid: 11 x 11 x 9 cells
> and then the simulation stops randomly without any messages besides the
> lam-mpi ones.
> does anyone have ideas?
> thanks
> loris...
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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