[gmx-users] (no subject) - fluctuations

[David van der Spoel]

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: spoel at xray.bmc.uu.se
>  > To: gmx-users at 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.Warren at pharm.monash.edu.au
>  > > > Subject: RE: [gmx-users] (no subject) - fluctuations
>  > > > To: gmx-users at 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.warren at 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.
>  > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se