[gmx-users] parinello-rahman coupling
Loris.Moretti at pharm.unige.ch
Tue Mar 27 16:44:31 CEST 2007
I set the pressure in the parameter file to be 1bar and I get different
average values ranging from 0.4 to 1.7 bar. Maybe they are not significantly
different (?) but I try to simulate large conformational changes and
what I saw small difference in settings can make different trajectories.
In my simulations Berendsen barostat can keep the mean value of the
according to the manual it does not yield a correct thermodynamic ensemble.
Tsjerk Wassenaar wrote:
> Hi Lorix,
> Sorry for that. You used the word "maintained" from which I inferred
> you were referring to the fluctuations (biased by the occurrence of
> the question obviously). Under normal conditions the equilibration
> shouldn't take that long. How far off is the mean? Do you still
> observe a trend? Still note that you're dealing with enormous, both
> positive and negative, pressures, from which you try to extract an
> average value. Such an average will usually not be very exact because
> of the numerical inaccuracies.
> On 3/27/07, lorix <Loris.Moretti at pharm.unige.ch> wrote:
>> 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
>> >> 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
>> >> 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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