Antonia V. wrote:
Hello,
I am interested mainly in the density.
When using parinello-rahman and nose-hoover the fluctuations are
approximately +/- 8. But when I am using Berendsen it falls to +/- 3.
I wanted to know if there is a way to reduce the fluctuation width of
the first case.
The density fluctuations in Berendsen are artificially small, so PR ones
should be more realistic. This is important when computing properties
like compressibility.
Antonia
> Date: Tue, 24 Mar 2009 09:49:45 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject) - fluctuations
>
> Antonia V. wrote:
> > Hello,
> >
> > So a I can either increase my system size or do some post
> > precessing-smoothing...
>
> If you elaborate on which properties you are interested in it may be
> possible to come up with more tips.
> >
> > Thanks for the ideas
> > Antonia
> >
> > > Date: Tue, 24 Mar 2009 11:39:19 +1100
> > > From: dallas.war...@pharm.monash.edu.au
> > > Subject: RE: [gmx-users] (no subject) - fluctuations
> > > To: gmx-users@gromacs.org
> > >
> > > > > Is there a way to reduce the fluctuations of the properties
> > > > calculated
> > > > > with g_energy?
> > >
> > > > Fluctuations scale as 1/sqrt(N) where N is the number of
> > > > molecules. So
> > > > the answer is yes.
> > >
> > > Depending on what you actually want to do, some smoothing of the data
> > > may be what you are after. One way of doing this is taking some
points
> > > before and after a time, then averaging them all together.
> > >
> > > Catch ya,
> > >
> > > Dr. Dallas Warren
> > > Department of Pharmaceutical Biology and Pharmacology
> > > Pharmacy and Pharmaceutical Sciences, Monash University
> > > 381 Royal Parade, Parkville VIC 3010
> > > dallas.war...@pharm.monash.edu.au
> > > +61 3 9903 9167
> > > ---------------------------------
> > > When the only tool you own is a hammer, every problem begins to
resemble
> > > a nail.
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> --
> 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.
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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