[gmx-users] parinello-rahman coupling

lorix Loris.Moretti at pharm.unige.ch
Tue Mar 27 14:44:20 CEST 2007

Hi Tsjerk,

Thanks for your prompt reply.
I was asking about the average value of the property.
I understood that large fluctuations are reasonable, but I was expecting 
that the mean value
over 15 ns could be somehow as the set in the parameter file as happens 
with Berendsen pressure coupling.
I checked the archives and I did not find much about the mean value.

best regards,


Tsjerk Wassenaar wrote:

> 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,
> Tsjerk
> 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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